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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagatggcatgtattaactaatgatcctttgttaatgcatgcatgtttaatcctctattggtaccgaggagtcgtgttataacctatgattgttttgcagTGGATCTTCTGGGTCGGCCCCTTCATTGGCGCTGCTCTGGCTGCCATCTACCACCAGGTGATCATCAGAGCCATCCCGTTCAAGAGCAGGTCTTAA

Basic information

species Zea mays
transcript AC209208.3_FGT002
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC209208.3_FGT002 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g44630.3 (Oryza sativa), 3'ss of exon 2
tagatggca-tgtattaactaatgatcctttgttaatgcatgcatgtttaatcctctattggtaccgaggagtcgtgttataacctatgattgttttgcagTGGATCTTCTGGGTCGGCCCCTTCATTGGCGCTGCTCTGGCTGCCATCTACCACCAGGTGATCATCAGAGCCATCCCGTTCAAGAGCAGGTCTTAA----
||  | | |   ||  | || |  | |||||| | | | |   | ||  ||  | | |     |        |       |    |||     |||||||||||||||||||||| || |||||| |||||||||| |||||||||||||||||||||||||||||||| || ||||| ||||||||||||||||||    
tacttagtagcttaccagcttactagcctttgctcaagaaaaga-gtagaagacacgacaaagagtttttccttacaaattttggtatctaaattttgcagTGGATCTTCTGGGTTGGTCCCTTCGTTGGCGCTGCCCTGGCTGCCATCTACCACCAGGTGATCATCAGGGCGATCCCATTCAAGAGCAGGTCTTAAGCCC

upper sequence: AC209208.3_FGT002 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G42220.3 (Glycine max), 3'ss of exon 3
-----------------------------tagatggcatgtatt--aactaatg-atcctttgttaatgcatgcatgttt----aatcctctattggtaccgaggagtc--gtg-ttataacctatgattgttt-tgcagTGGATCTTCTGGGTCGGCCCCTTCATTGGCGCTGCTCTGGCTGCCATCTACCACCAGGTGATCATCAGAGCCATCCCGTTCAAGAGCAGGT--CTTAA--
                             ||  ||  || | ||  |  | | | |   |||||  |    |  || |||    ||  |     |||| |    || ||   || ||||    | |  || | | ||||||||||||||||||| || || |||||||| ||||| || || ||  |||||||||||||  | ||||| ||||| || ||||||  || ||   | ||  
gtaagttgttaattgattcatttatttcataattgctatttttttcattttacgcaatatttgtccaattttagatttttcgggaaaacgaatctggtccgtctgattctgatgcttattgtttgtcgttttctgtgcagTGGATCTTCTGGGTGGGACCTTTCATTGGTGCTGCACTTGCAGCACTCTACCACCAGGTCGTAATCAGGGCCATTCCCTTCAAGTCCAAGTGATTCAATC

upper sequence: AC209208.3_FGT002 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA14G06680.2 (Glycine max), 3'ss of exon 2
-----------------------------tagatggcatgtattaa--ctaatgatcctttgttaatgcatgcatgtttaatcctctattggtaccgaggagtcgtg-ttataacctatgattgttt-tgcagTGGATCTTCTGGGTCGGCCCCTTCATTGGCGCTGCTCTGGCTGCCATCTACCACCAGGTGATCATCAGAGCCATCCCGTTCAAGAGCAGGT--CTTAA--
                             ||  ||| |   |  ||    | ||| ||  | |||     | |  |   |    |||   |     ||    |   | ||||    | |  || |   ||||||||||||||||||| || || ||||| || || ||||| || ||  |||||||||||||  | ||||| ||||| || ||||||  || ||   | ||  
gtaagttgttaattaattcatttatttcataattggtaaaaaaaaaaatcattgaaccaattttagatttttcgggaaaacgaatctggagcgtttgatctctgacgcttattgtttgtcgttttccgtgcagTGGATCTTCTGGGTGGGACCATTCATCGGTGCAGCTCTTGCAGCACTCTACCACCAGGTCGTAATCAGGGCCATTCCCTTCAAGTCCAAGTGATTCAATC

upper sequence: AC209208.3_FGT002 (Zea mays), 3'ss of exon 3
lower sequence: Vv15s0046g02420.t01 (Vitis vinifera), 3'ss of exon 3
-tagatggcatgtattaact-aatgatcctttgttaatgcatgcatgtttaatcctctattggtaccgaggagtcgtgttataacctatgattgttttgcagTGGATCTTCTGGGTCGGCCCCTTCATTGGCGCTGCTCTGGCTGCCATCTACCACCAGGTGATCATCAGAGCCATCCCGTTCAAGAGCAGGTCTTAA----
 ||     ||||     ||  ||| |    |  |     |||  || | | |  ||   ||| ||  ||    |    || |    | |  ||   || |||||||| |||||||| || ||||||||||| |||||||| |||||| | ||||||||| |  | |||||||||||||| ||||||| |||  | | |    
gtaagctccatgatcagacccaatcacttctcatctcatcatttatctgtgaatctgccttg-tattga----tttcattct--tttgttgttccctt-cagTGGATTTTCTGGGTTGGACCCTTCATTGGAGCTGCTCTTGCTGCCTTGTACCACCAGATAGTAATCAGAGCCATCCCATTCAAGACCAGAGCCTGAGAAA

upper sequence: AC209208.3_FGT002 (Zea mays), 3'ss of exon 3
lower sequence: Vv15s0046g02410.t01 (Vitis vinifera), 3'ss of exon 3
-tagatggcatgtattaactaatgatcctttgttaatgcatgcatgtttaatcctctattggtaccgaggagtcgtgttataacc--tatgattgttttg--cagTGGATCTTCTGGGTCGGCCCCTTCATTGGCGCTGCTCTGGCTGCCATCTACCACCAGGTGATCATCAGAGCCATCCCGTTCAAGAGCAGGTCTTAA----
 ||  ||  |   |||     || |         |||   | |   | |  || |||||  ||      || | || ||     |  | |  |||||     |||||||| |||||||| || ||||||||||| ||| |||||||| || | ||||||||| |  |||||||||| ||||| ||||||| |||  | | |    
gtaagtgaaa-acattgctctataagaagac-ccaatagcttctcatctcgtcatctatctgtgaatctgacttgtattgatttcattcttgttgttcccatcagTGGATTTTCTGGGTTGGACCCTTCATTGGAGCTACTCTGGCTACCTTGTACCACCAGATAGTCATCAGAGCTATCCCATTCAAGACCAGAGCCTGAGAAA

upper sequence: AC209208.3_FGT002 (Zea mays), 3'ss of exon 3
lower sequence: Vv02s0025g03390.t01 (Vitis vinifera), 3'ss of exon 3
---------tagatggcatgtattaactaa----tgatcctttgttaatgcatgcatgtttaatcctctattggtaccgaggagtcgtgttataacctatgattgttt---tgcagTGGATCTTCTGGGTCGGCCCCTTCATTGGCGCTGCTCTGGCTGCCATCTACCACCAGGTGATCATCAGAGCCATCCCGTTCAAGAGCAGGTCTTAA----
         | ||||  |   |  ||  ||    | |    || |  || | |  ||| ||||       ||     | ||   || | || | || | |  |   ||   | ||||||||||||||||| || || |||||||| |||||||| |||||||| ||||| ||| |  ||||||||||||| || |||||||||||| ||| |    
gtaggtgttttgatgagaaaaaaaaaaaaaaacctaaggaattttgcatcctttgatggttaaattgagtttcagttcaag--ttcttattgtgactttttttctcttgctttcagTGGATCTTCTGGGTGGGACCGTTCATTGGAGCTGCTCTTGCTGCCATGTACCAGCAGATAGTCATCAGAGCCATTCCATTCAAGAGCAGGGCTTGAGATT

upper sequence: AC209208.3_FGT002 (Zea mays), 3'ss of exon 3
lower sequence: Vv13s0067g00220.t01 (Vitis vinifera), 3'ss of exon 3
---------------------tagatggcatgtattaactaatgatcctttgttaatgcatgcatgtttaatcctc-tattggtaccgaggagt-cgtgttataacctatgattgttt-----tgcagTGGATCTTCTGGGTCGGCCCCTTCATTGGCGCTGCTCTGGCTGCCATCTACCACCAGGTGATCATCAGAGCCATCCCGTTCAAGAGCAGGTCTTAA-
                     |  |   ||| | ||  ||     |  | |  || |  |  ||   | |    |  |  |  | |  | |  | | | || |   || | | ||  |     | ||||||||||||||||| || || |||||||| || || || || ||  | |||||||||||| ||||||||||||| || ||||||  || ||  | | 
gtaagccaccgattgggcttctctacttcattttttc-ctttcccttttcttctagtcaactcacaataatcaatagtgctaatgcttatggttgccttttcttttcttttactgcctcatgctacagTGGATCTTCTGGGTGGGACCATTCATTGGGGCCGCACTAGCAGCTTTATACCACCAGGTGGTCATCAGAGCCATTCCCTTCAAGTCCAAGTGATGAT

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|149094560|gb|EE180082.2|EE180082
EST:     GCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCAT                         TGGATCTTCTGGGTCGGCCC
genomic: GCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCATgtgagtggaa ... tgttttgcagTGGATCTTCTGGGTCGGCCC
EST: gi|213172229|gb|FM182804.1|FM182804
EST:     GCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCAT                         TGGATCTTCTGGGTCGGCCCCTTCATTGGCGCTGCCCTGGCTGCCATCTAC
genomic: GCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCATgtgagtggaa ... tgttttgcagTGGATCTTCTGGGTCGGCCCCTTCATTGGCGCTGCTCTGGCTGCCATCTAC
EST: gi|148982069|gb|EE028110.2|EE028110
EST:     GCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCAT                         TGGATCCTCTGGGTCGCCCCCTTCATTGGCGCTGCTCTGGCTGCCATCTA
genomic: GCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCATgtgagtggaa ... tgttttgcagTGGATCTTCTGGGTCGGCCCCTTCATTGGCGCTGCTCTGGCTGCCATCTA
EST: gi|149046894|gb|EE048104.2|EE048104
EST:     GCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCAT                         TGGATCTTCTGGGTCGGCCCC
genomic: GCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCATgtgagtggaa ... tgttttgcagTGGATCTTCTGGGTCGGCCCC

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 525

CCACCTTGCCACCATCCCCATTACTGGCACTGGCATCAACCCAGCTAGGAGCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCATgtgagtggaa ... tgttttgcagTGGATCTTCTGGGTCGGCCCCTTCATTGGCGCTGCTCTGGCTGCCATCTACCACCAGGTGATCATCAGAGCCATCCCGTTCAAGAGCAGGTCTTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 674

CCACCTTGCCACCATCCCCATTACTGGCACTGGCATCAACCCAGCTAGGAGCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCATgtgagtggaa ... tgttttgcagTGGATCTTCTGGGTCGGCCCCTTCATTGGCGCTGCTCTGGCTGCCATCTACCACCAGGTGATCATCAGAGCCATCCCGTTCAAGAGCAGGTCTTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 944

CCACCTTGCCACCATCCCCATTACTGGCACTGGCATCAACCCAGCTAGGAGCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCATgtgagtggaa ... tgttttgcagTGGATCTTCTGGGTCGGCCCCTTCATTGGCGCTGCTCTGGCTGCCATCTACCACCAGGTGATCATCAGAGCCATCCCGTTCAAGAGCAGGTCTTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 682

CCACCTTGCCACCATCCCCATTACTGGCACTGGCATCAACCCAGCTAGGAGCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCATgtgagtggaa ... tgttttgcagTGGATCTTCTGGGTCGGCCCCTTCATTGGCGCTGCTCTGGCTGCCATCTACCACCAGGTGATCATCAGAGCCATCCCGTTCAAGAGCAGGTCTTAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaatcctctattggtaccgaggagtcgtgttataacctatgattgttttgcagTGGATCTTCTGGGTCGGCCCCTTCATTGGCGCTGCTCTGGCTGCCATCTACCACCAGGTGATCATCAGAGCCATCCCGTTCAAGAGCAGGTCTTAA
                               ttataac  putative branch site (score: 682)
                                            ttgtttt  putative PPT
                             tgttataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagatggcatgtattaactaatgatcctttgttaatgcatgcatgtttaatcctctattggtaccgaggagtcgtgttataacctatgattgttttgcagTGGATCTTCTGGGTCGGCCCCTTCATTGGCGCTGCTCTGGCTGCCATCTACCACCAGGTGATCATCAGAGCCATCCCGTTCAAGAGCAGGTCTTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - gcatgta
- - - - - - - - - - -tgatcct
- - - - - - - - - - - - - - - - - -tgcatgc