Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcttccagccttttcgttttctttccacgctcaaactttcacggtcgagtccatagtcatagtttttgttctagtacacttgactgactagactttctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCATGGACGGCGGCCGCGACACGGAGATCGCCATGGGAGCGTACCAGCCGTT

Basic information

species Selaginella moellendorffii
transcript EFJ06378
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ06378 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os06g40180.1 (Oryza sativa), 3'ss of exon 2
gtaagtcttccagccttttcgttttctttccacgctcaaactttcacggtcgagtccatagtcatagtttttgttctagtacacttgactgactagactttctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCATGGACGGCGGCCGCGACACGGAGATCGCCATGGGAGCGTACCAGCCGTT
           | |     | |  |  || ||   |  |||    |||||  |   |    ||  | |||          ||||   | | | | |  |||||  || |||| || || |||||||||||||||||||||||||||||||||||||| || ||||||||||| || ||| ||||||||||||||||||||| ||||||   
---------gtaacaacaac-tactagttgcaaatttcaaccactacggttaaactcgc--tctaaatttc---------acaccgaattcaat-gtttttcttttatcagTTGATGATGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGGTCGATGGACGGCGGGCGGGACTCGGAGATCGCCATGGGAGCGTTCCAGCCACA

upper sequence: EFJ06378 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os03g27370.1 (Oryza sativa), 3'ss of exon 3
gtaagtcttccagccttttcgttttctttccacgctcaaact--ttcacggtcg-agtccatagtcatagtttttgttctagtacacttgactgactagactttctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCATGGACGGCGGCCGCGACACGGAGATCGCCATGGGAGCGTACCAGCCGTT
           |   || |  ||| |     | |    ||    || ||  ||  | || ||      |  | | ||  |  | | ||        | ||  |  | |||   ||||||||||||||||||||||| |||||||| |||||||||||| | || ||||||||||| || |||||||||||||| ||||| ||||||||||||  
-----------atgtttatattttgcaacggatggagtaatcaattgacaatcttaatcaatctaagaacatgtcgtcgtgatgctctgtttctgttcgatctatttgta---gTGGACGACGAGTACATCATCGTGGGGTCGGCGAACATCAACCAGAGGTCGATGGACGGCGGGCGGGACACGGAGATCGCGATGGGCGCGTACCAGCCGAG

upper sequence: EFJ06378 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os05g07880.1 (Oryza sativa), 3'ss of exon 3
gtaagtcttccagccttttcgttttctttccacgctcaaactttcacggtcgagtccatagtcatagtttttgttctagtacacttgactgactagactttctcgt-aacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCATGGACGGCGGCCGCGACACGGAGATCGCCATGGGAGCGTACCAGCCGTT
                                ||   | |  | |  | | ||    |     || |||||||      |   |||||  || | |  | | |  | | |||||||||||||||||||||||||||||||||| |||||||||||| | || |||||||| |   | ||| |||||||||||||||||||||||||||||  
-----------------------------gttcgtatatatctcc-tgattgatcttaccacgattgtttttggatgcattt-cttgatcgatttggttgtgtgttcatcagTGGACGACGAGTACATCATCGTCGGGTCGGCGAACATCAACCAGAGGTCGATGGACGGGGCGAGGGACTCGGAGATCGCCATGGGAGCGTACCAGCCGCA

upper sequence: EFJ06378 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os06g40170.1 (Oryza sativa), 3'ss of exon 2
gtaagtcttccagccttttcgttttctttccacgctcaaactttcacggtcgagtccatagtcatagtttttgttctagtacacttgactgactagactttctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCATGGACGGCGGCCGCGACACGGAGATCGCCATGGGAGCGTACCAGCCGTT
       |   ||     | | |   |    | | || ||  | |    ||  |||  | |  |    |  | ||| |  |   || |   | |    |   | ||  |||| || ||||||||||||||||| || |||||||||||||||||| | || |||||||||||||| ||| ||||||||||||||||||| | ||||||   
------ataatagatagatagatagatag--atgttctaatgtgctta-tcatgtcatttggtacctgtacttttcaaaaagtttttaaaaattg--ttcgtttgtttcagTCGATGACGAGTACATCATCGTGGGATCGGCCAACATCAACCAGAGGTCGATGGACGGCGGCCGAGACTCGGAGATCGCCATGGGAGCATTCCAGCCACA

upper sequence: EFJ06378 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os06g40190.1 (Oryza sativa), 3'ss of exon 2
gtaagtcttccagccttttcgttttctttccacgctcaaactttcacggtcgagtccatagtcatagtttttgttctagtacacttgactgactagactttctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCATGGACGGCGGCCGCGACACGGAGATCGCCATGGGAGCGTACCAGCCGTT
        |   | |  |   | || ||||    |     |||| | |      | |||  | |||    |   | |  |  |  | | |  |     |||   ||  |||| ||||||||||||||||| || || || ||||||||||||||| | |||||||| || ||| | ||| | |||||||||||||| || | |||||| | 
--------tattgtcactggctcttatttcagtacctgtgctttgatgacatgcttcatgttgataaagataaatttgttggaacttaatatccttggttt---gtttcagTTGACGACGAGTACATCATTGTTGGATCTGCCAACATCAACCAGAGGTCCATGGATGGGGGCAGAGACTCCGAGATCGCCATGGGTGCATTCCAGCCATG

upper sequence: EFJ06378 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os01g07760.1 (Oryza sativa), 3'ss of exon 3
gtaagtcttccagccttttcgttttctttccacgctcaaactttcacggtcgagtccatagtcatagtttttgttctagtacacttgactgactagactttctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCATGGACGGCGGCCGCGACACGGAGATCGCCATGGGAGCGTACCAGCCGTT
 | |     | ||    ||| | | |||     | |     |||  |  || |    |||  | || | ||    |||||| |||| | |   |  | ||||       ||| ||||| |||||||||||| |||| || || |||||||||||| | || ||||||||||   | ||| | |||||||||||||| | ||||||||| | 
-tgatcaagctagtaacttcatctccttattcggtttc--ttttttctatcaaaaatatacacttattgttcaagctagta-acttcatttcttccattttc-------agTTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGATGGACGGCGCTAGGGACTCTGAGATCGCCATGGGCGGGTACCAGCCATA

upper sequence: EFJ06378 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G179792_T02 (Zea mays), 3'ss of exon 3
gtaagtcttccagccttttcgttttctttccacgctcaaactttcacggtcgagtccatagtcatagtttttgttctagtacacttgactgactagactttctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCATGGACGGCGGCCGCGACACGGAGATCGCCATGGGAGCGTACCAGCCGTT
                            | ||| | | |     |||| |  |      | | |||    | | |   ||||   |||  |    ||||  |    | |||||||||| |||||||||||||| || ||||| ||||||||||||||||||||||||||||||||||||||||||||||| ||||| ||||||||||||  
---------------------------gtacacacacga-----cacgattcatctagcaataataacaatggcttccgtacgtctga--ggtctgactcgcg---agcagTGGACGATGAGTACATCATCGTGGGCTCGGCGAACATCAACCAGCGCTCCATGGACGGCGGCCGCGACACGGAGATCGCGATGGGCGCGTACCAGCCGGG

upper sequence: EFJ06378 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G019029_T01 (Zea mays), 3'ss of exon 2
gtaagtcttccagccttttcgttttctttccacgctcaaactttcacggtcg-agtccatagtcatagtttttgttctagtacacttgactgactagactttctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCATGGACGGCGGCCGCGACACGGAGATCGCCATGGGAGCGTACCAGCCGTT
                                   | |    || |||  |  | | | || | || ||||  ||   ||        ||||  | | | ||  |||  ||||||| ||||||||||||||||| || ||||| ||||||||||||||||||||||||||||||||||||||||||||||| || || ||||||||||||  
----------------------------------gtaatttattgacgaccataatacttactaatggtttccgtctgag--------actgg-tggtcgtttgcgtg-cagTGGATGACGAGTACATCATCGTGGGATCGGCGAACATCAACCAGCGCTCCATGGACGGCGGCCGCGACACGGAGATCGCGATCGGCGCGTACCAGCCGGG

upper sequence: EFJ06378 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G029896_T01 (Zea mays), 3'ss of exon 1
gtaagtcttccagccttttcgttttctt--tccacgctcaaactttcacggtcga---gtccatagtcatagt---ttttgttctagtacacttgactgactagac-tttctcgta---acagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCATGGACGGCGGCCGCGACACGGAGATCGCCATGGGAGCGTACCAGCCGTT
||||  | |||  ||        | ||      || ||  |  ||||    ||||   | ||||  || |||    | ||  ||| | |   ||  |  | | ||  |||   ||     ||||||| ||||||||||||||||| |||||||| |||||||||||||| ||||||||||| |  || ||| |||||||||| ||||| ||||||||||||  
gtaatccgtccgtccacccttactcctagaattactcttgatttttcgaattcgaggcgcccatcttcttagaatatattactcttgaattattatcaaaatcgaaatttgctgtgtgtgcagTGGATGACGAGTACATCATCGTGGGGTCGGCGAACATCAACCAGCGTTCCATGGACGGGGCGCGGGACTCGGAGATCGCGATGGGCGCGTACCAGCCGCA

upper sequence: EFJ06378 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G054559_T01 (Zea mays), 3'ss of exon 3
gtaagtcttccagccttttcgttttctttccacgctcaaactttcacggtcgagtccatagtcatagtttttgttctagtacacttgactgactagactttctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCATGGACGGCGGCCGCGACACGGAGATCGCCATGGGAGCGTACCAGCCGTT
       |      |  |    || ||        |    || ||  | | |     | || ||||  |||||||   | | |    |  || |    | | | ||  ||||||||||||||||||||||| | ||||| ||||||||||||||| | ||||||||||| | | | ||| | |||||||||||||| ||||||||||||| 
------gtgttgaacagtcaaattcctgcttgaatt---gctctcttgcttggtctgaaaggcatacattttgttgatgaagatggtaacgattt--ttgtttggtttcagTGGACGACGAGTACATCATCATTGGGTCCGCCAACATCAACCAGAGGTCCATGGACGGTGCCAGGGACTCCGAGATCGCCATGGGCGCGTACCAGCCGTA

upper sequence: EFJ06378 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G442551_T02 (Zea mays), 3'ss of exon 2
gtaagtcttccagcct--tttcgttttctttccacgctcaaactttcacggtcgagtccatagtcatagtttttgttctagtacacttgactgactagactttctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCATGGACGGCGGCCGCGACACGGAGATCGCCATGGGAGCGTACCAGCCGTT
          | ||||  |  |||   ||   |         | | ||| ||    |  |  ||   |||||    | ||  ||   |||    | |  || ||| ||  |||| |||||||| ||||||||||| || || ||||| |||||||||||||| ||||| || ||| | ||| |||||||||||||||| ||||||||||||| 
----------ctgcctgataccgtcgcctaatcttatcagttcctacacagtttcatgtaaggttcgagtttaacgtttataacctgtgatctgcca--ctctct-gttgcagTCGACGACGAATACATCATCGTTGGATCTGCCAATATCAACCAGCGCTCAATGGATGGGGGCAGGGACTCGGAGATCGCCATGGGCGCGTACCAGCCGTG

upper sequence: EFJ06378 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G061969_T02 (Zea mays), 3'ss of exon 4
gtaagtcttccagccttttcgttttctttccacgctcaaactttcacggtcgagtccatagtcatagtttttgttctagtacacttgactgactagactttctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCATGGACGGCGGCCGCGACACGGAGATCGCCATGGGAGCGTACCAGCCGTT
   ||| ||  |||       ||     |  |   ||    | ||  | | |  |    || |||    |||  |   | | |    |   | |   || | |  |  |||||||||| || ||||||||| | ||||| ||||||||||||||| | ||||||||||| | | | ||| | ||||| |||||||| ||||||||||||| 
---agtgttg-agcagccgaattcctacttgaatttc----tctcttgcttggcttggaaggcatc-catttactgacgaagatggtaacaattt--ctgtttgatttcagTGGACGATGAATACATCATCATTGGGTCCGCCAACATCAACCAGAGGTCCATGGACGGTGCCAGGGACTCCGAGATAGCCATGGGCGCGTACCAGCCGTA

upper sequence: EFJ06378 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv04s0008g05450.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtc-ttccagccttttcgttttctttccacgctcaaactttcacggtcgagtccatagtcatagtttttgttctagtacacttgactgactagactttctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCATGGACGGCGGCCGCGACACGGAGATCGCCATGGGAGCGTACCAGCCGTT
||||||| |  | ||   |||  |||| ||| ||   ||  ||||  ||||     | ||  |||| || | ||||   ||             | |  ||| ||     ||||||||| |||||||| ||| | ||||||||||||||||||||| | || ||||| || ||  | ||||| ||||| |||||||||| |||||||||   
gtaagtcataactgcagcttctatttccttcaacttgcattcttt-gcggta----ctatgttcat-gtgtgtgtttgtgt-------------ttggttttttc-----agTGGACGATGAGTACATAATCATTGGGTCGGCCAACATCAACCAGAGGTCAATGGATGGTGGGAGAGACACAGAGATAGCCATGGGAGGGTACCAGCCACA

upper sequence: EFJ06378 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S10_149V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaagtcttccagccttttcgttttctttccacgctcaaactttcacggtcgagtccatagtcatagtttttgttctagtacacttgactgactagactttctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCATGGACGGCGGCCGCGACACGGAGATCGCCATGGGAGCGTACCAGCCGTT
|| ||| | | | |  ||  |  |  | |  |  |||   ||  ||||  |     | | || ||  |   ||| ||| |  ||     ||||     |  | | |  |||||||||||||||| || || || |||||||||||||||||| || | ||| || |||| |  || ||| | ||||| |||||||| || ||||||||   
gtgagtatacaacctcttcagcctcatctagatactcttgct--cacg--catactctttgtgattctacatgtgctaatgaaccc--ttgacattgttcccgcctg-cagTGGACGACGAGTATATAATAGTGGGGTCGGCCAACATCAACGAGAGGTCCTTGAACGGTGCGCGTGACTCTGAGATTGCCATGGGGGCTTACCAGCCTCA

upper sequence: EFJ06378 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S94_26V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaagtcttccagccttttcgttttctttccacgctcaaactttcacggtcgagtccatagtcatagtttttgttctagtacacttgactgactagact-ttctcgta-acagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCATGGACGGCGGCCGCGACACGGAGATCGCCATGGGAGCGTACCAGCCGTT
|| ||| ||      | ||  |    ||       |||  ||| ||     || |    | |   | || ||    |  |||   ||||  ||     | ||   |   |||||||| ||||||||||| || || ||||| |||||||||||| || | ||| || |||| |  |||||| | || || ||||||||||| || |||||   
gtgagtatttttatgtcttactcagattcatttattcacgcttacaaaaaagaattttcaatgtcatttgttcccttgctactggtgacgaacccttttgttgctgcgtacagTGGATGACGAGTACATAATAGTGGGGTCAGCCAACATCAACGAGAGATCCTTGAACGGTGCACGCGACTCCGAAATTGCCATGGGAGCTTATCAGCCTCA

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|169078586|gb|FE490723.1|FE490723
EST:     ACAGGAGCACAGGAGGTTCATGATCTACGTTCACTCCAAGATGATGATCG                         TGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCA
genomic: ACAGGAGCACAGGAGGTTCATGATCTACGTTCACTCCAAGATGATGATCGgtaagtcttc ... ctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCA
EST: gi|169043032|gb|FE452386.1|FE452386
EST:     ACAGGAGCACAGGAGGTTCATGATCTACGTTCACTCCAAGATGATGATCG                         TGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCA
genomic: ACAGGAGCACAGGAGGTTCATGATCTACGTTCACTCCAAGATGATGATCGgtaagtcttc ... ctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCA
EST: gi|169058412|gb|FE466309.1|FE466309
EST:     ACAGGAGCACAGGAGGTTCATGATCTACGTTCACTCCAAGATGATGATCG                         TGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCA
genomic: ACAGGAGCACAGGAGGTTCATGATCTACGTTCACTCCAAGATGATGATCGgtaagtcttc ... ctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCA
EST: gi|169087426|gb|FE494595.1|FE494595
EST:     ACAGGAGCACAGGAGGTTCATGATCTACGTTCACTCCAAGATGATGATCG                         TGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCA
genomic: ACAGGAGCACAGGAGGTTCATGATCTACGTTCACTCCAAGATGATGATCGgtaagtcttc ... ctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCA
EST: gi|169099143|gb|FE502852.1|FE502852
EST:     ACAGGAGCACAGGAGGTTCATGATCTACGTTCACTCCAAGATGATGATCG                         TGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCA
genomic: ACAGGAGCACAGGAGGTTCATGATCTACGTTCACTCCAAGATGATGATCGgtaagtcttc ... ctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCA
EST: gi|169063174|gb|FE471696.1|FE471696
EST:     ACAGGAGCACAGGAGGTTCATGATCTACGTTCACTCCAAGATGATGATCG                         TGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCA
genomic: ACAGGAGCACAGGAGGTTCATGATCTACGTTCACTCCAAGATGATGATCGgtaagtcttc ... ctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCA
EST: gi|169111504|gb|FE510364.1|FE510364
EST:     ACAGGAGCACAGGAGGTTCATGATCTACGTTCACTCCAAGATGATGATCG                         TGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCA
genomic: ACAGGAGCACAGGAGGTTCATGATCTACGTTCACTCCAAGATGATGATCGgtaagtcttc ... ctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCA
EST: gi|169103898|gb|FE508382.1|FE508382
EST:     ACAGGAGCACAGGAGGTTCATGATCTACGTTCACTCCAAGATGATGATCG                         TGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCA
genomic: ACAGGAGCACAGGAGGTTCATGATCTACGTTCACTCCAAGATGATGATCGgtaagtcttc ... ctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCA
EST: gi|169025648|gb|FE436561.1|FE436561
EST:     ACAGGAGCACAGGAGGTTCATGATCTACGTTCACTCCAAGATGATGATCG                         TGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCA
genomic: ACAGGAGCACAGGAGGTTCATGATCTACGTTCACTCCAAGATGATGATCGgtaagtcttc ... ctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCA
EST: gi|169098908|gb|FE502305.1|FE502305
EST:     ACAGGAGCACAGGAGGTTCATGATCTACGTTCACTCCAAGATGATGATCG                         TGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCA
genomic: ACAGGAGCACAGGAGGTTCATGATCTACGTTCACTCCAAGATGATGATCGgtaagtcttc ... ctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCA
EST: gi|169046516|gb|FE457455.1|FE457455
EST:     ACAGGAGCACAGGAGGTTCATGATCTACGTTCACTCCAAGATGATGATCG                         TGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCA
genomic: ACAGGAGCACAGGAGGTTCATGATCTACGTTCACTCCAAGATGATGATCGgtaagtcttc ... ctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 34 (downstream exon)
Score: 30

TACGTCCCGCCGGAGGCCATCGAGGAGGAGGCAACGAACTACAAGGCAGCACAGGAGCACAGGAGGTTCATGATCTACGTTCACTCCAAGATGATGATCGgtaagtcttc ... ctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCATGGACGGCGGCCGCGACACGGAGATCGCCATGGGAGCGTACCAGCCGTT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catagtcatagtttttgttctagtacacttgactgactagactttctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCATGGACGGCGGCCGCGACACGGAGATCGCCATGGGAGCGTACCAGCCGTT
                              gactgac  putative branch site (score: 30)
                                         ctttctcgt  putative PPT
       atagttttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcttccagccttttcgttttctttccacgctcaaactttcacggtcgagtccatagtcatagtttttgttctagtacacttgactgactagactttctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCATGGACGGCGGCCGCGACACGGAGATCGCCATGGGAGCGTACCAGCCGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC