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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatactcatactcagctttaatataagttgattttttatagtgcattattttttgttaatcctctgcatcagttgataaaatccatcctctatatgcagCTTCTTGGGCGAAGCGGCGGGTTTCAAGTGGCTTCAACACATCGGCCTTGCACCAAAGGACTTTGGATGTGGAGTGCGCCTTTGAAGAGAACTGGTCTGG

Basic information

species Zea mays
transcript GRMZM2G031053_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031053_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA13G24260.1 (Glycine max), 3'ss of exon 1
tcatactcatactcagctttaatataagttgattttttatagtgcattattttttgttaatcctctgcatcagt-tgataaaatccatcctctatatg-cagCTTCTTGGGCGAAGCGGCGGGTTTCAAGTGGCTTCAACACATCGGCCTTGCACCAAAGGACTTTGGATGTGGAGTGCGCCTTTGAAGAGAACTGGTCTGG
     ||       ||  || | |||   | | |   || ||||     || ||   |  |  |    ||| || |  |    |   |  | | |||  |||||  | ||    ||  | || |||||||| || ||||||||||||||||| |||||||| |||||| |||||||||| ||||||||||  |||| ||| |
-tccgctttctgcaagtattgaaatacaattactaaata-agtgagactttgttaaattgttattataatctgtattgtgtcttatgttttttgtatttcagCTCTTAGGAAAGAGTAGTGGATTTCAAGTAGCATCAACACATCGGCCTTGTACCAAAGGGCTTTGGTTGTGGAGTGCACCTTTGAAGAAGACTGCTCTTG

upper sequence: GRMZM2G031053_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA13G30780.1 (Glycine max), 3'ss of exon 1
--tcatactcatactcagctttaatataagttgattttttatagtgcattattttttgttaatcctctgcatcagttgataaaatccatcctctatatgcagCTTCTTGGGCGAAGCGGCGGGTTTCAAGTGGCTTCAACACATCGGCCTTGCACCAAAGGACTTTGGATGTGGAGTGCGCCTTTGAAGAGAACTGGTCTGG
  ||  | |  |    | ||    | |     ||||  ||| |      |  |  |    |    |  |  |  |||   |  | ||     ||   |||||||| | ||| | |   | || ||||| || || ||||||||||| || || ||||||||||| ||| |||||||||| || |||||||| ||||  || |
agtctcattt-tgagtaactactttgtgcacagattactta-aacagtctggtgataaaaagagttgagactgtgttctcattaccctaatccttattgcagCTTTTGGGGAGGACTAGTGGATTTCAGGTAGCATCAACACATCGACCATGTACCAAAGGACTATGGTTGTGGAGTGCACCGTTGAAGAGGACTGCCCTTG

upper sequence: GRMZM2G031053_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA07G32290.2 (Glycine max), 3'ss of exon 1
-tcatactcatactcagctttaatataagttgattttttatagtgcattattttttgttaatcctctgcatcagttgataaaatccatcctctatatgcagCTTCTTGGGCGAAGCGGCGGGTTTCAAGTGGCTTCAACACATCGGCCTTGCACCAAAGGACTTTGGATGTGGAGTGCGCCTTTGAAGAGAACTGGTCTGG
 |   ||| |   || |||    |  || |  | ||  || | |   | |   |||||||      |     | |   ||   |   |  |     | |||||  | ||    ||  |||| |||||||| || |||||||||||||| ||||||||||| |||||| |||||||||| ||||||||||  || | ||| |
tttccactgactttctgctggtgttgaaatacaattacta-aataagtgagactttgttagattgttattataatctgtattgtggctttttgcatttcagCTCTTAGGAAAGAGTAGCGGATTTCAAGTAGCCTCAACACATCGGCCATGCACCAAAGGGCTTTGGTTGTGGAGTGCACCTTTGAAGAAGACCGCTCTTG

upper sequence: GRMZM2G031053_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv10s0003g00370.t01 (Vitis vinifera), 3'ss of exon 1
--tcatactcatactcagctttaatataagttgattttttatagtgcattattttttgttaatcctctgcatcagttgataaaatccatcctctatatgcagCTTCTTGGGCGAAGCGGCGGGTTTCAAGTGGCTTCAACACATCGGCCTTGCACCAAAGGACTTTGGATGTGGAGTGCGCCTTTGAAGAGAACTGGTCTGG
     |||   | |||  | ||  |    |||   | | | ||    | | |||| ||| |   || |   |  ||  |     | ||| |  |   || ||||||||||| | ||  | ||||||||||| || ||||| |||||||| || |||||||| |||||| |||||||  | || || |||||||||| ||| |
aagtgtacctct-ctcctcattctttcctgttatatatctgta-caaaatgttttgtgtcacatctataactatgtgcactgcttgcatgcatttgttgtagCTTCTTGGGAGGAGTAGTGGGTTTCAAGTTGCATCAACTCATCGGCCATGTACCAAAGGGCTTTGGTTGTGGAGCACACCCTTAAAGAGAACTGCTCTTG

upper sequence: GRMZM2G031053_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S74_251V6.1 (Physcomitrella patens), 3'ss of exon 1
tcatactcatactcagctttaatataagttgattttttatagtgcattattttttgttaatcctctgcatcagttgataaa-atccatcctctata--tgcagCTTCTTGGGCGAAGCGGCGGGTTTCAAGTGGCTTCAACACATCGGCCTTGCACCAAAGGACTTTGGATGTGGAGTGCGCCTTTGAAGAGAACTGGTCTGG
   |    ||     | | ||  |  | |    |   || |||        | ||  || |  |    |  || ||||||   | ||||||| |    |  |||| || || |  |||   |||||| |||| ||  | || ||   ||||||||| ||||||||||||||||||||||| ||| | ||| | || | |   |
ggctggagatgtaaggttgtatcaataatcatgtaactaaagtctggagcctgtt-ctagt--tgaatactagctgataattgtacatcctccacgactttagCTGCTAGGACAGAGCAATGGGTTTGAAGTTGCGGCTACTCAGAAGCCTTGCACGAAAGGACTTTGGATGTGGAGTGCACCTATTAAGCGTACAGCTGCAG

upper sequence: GRMZM2G031053_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S391_33V6.1 (Physcomitrella patens), 3'ss of exon 1
tcatactcatactcagctttaat-ataagttgattttttatagtgcattattttttgttaatcctc-tgcatcagttgataaaatccatcctct-atatgcagCTTCTTGGGCGAAGCGGCGGGTTTCAAGTGGCTTCAACACATCGGCCTTGCACCAAAGGACTTTGGATGTGGAGTGCGCCTTTGAAGAGAACTGGTCTGG
   |    ||    | |   ||| || |||||  |   |      |    ||   | |||||| |  | |    ||  | ||    | |    | | |  ||||| || || |||||| |||||||| |||| || || || ||   ||| |||||||| |||||||||||||||||||| ||  | ||| |||| | || ||
---tgtaaatttcaaacggaaatgatgagttgtatcagttggacacggctttgacttttaatcgtaattcgggcgtgaacaatgaacgtttgatcaaaatcagCTGCTAGGACGAAGCAGCGGGTTTGAAGTTGCGTCTACCCAGAAGCCCTGCACCAAGGGACTTTGGATGTGGAGTGCACCCGTTAAGCGAACAGCTCCGG

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: 48 (upstream exon), 49 (downstream exon)
Score: 182

CCCCGAGGCGGTGGCCGCGCTGCAGCTCGTCAAGGGCCCCGTCGGGGTCGTCTCCGTCTGCGGCCGCGCGCGCCAGGGCAAGAGCTTCATCCTCAACCAGgtacgacgcg ... ctatatgcagCTTCTTGGGCGAAGCGGCGGGTTTCAAGTGGCTTCAACACATCGGCCTTGCACCAAAGGACTTTGGATGTGGAGTGCGCCTTTGAAGAGAACTGGTCTGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 105

CCCCGAGGCGGTGGCCGCGCTGCAGCTCGTCAAGGGCCCCGTCGGGGTCGTCTCCGTCTGCGGCCGCGCGCGCCAGGGCAAGAGCTTCATCCTCAACCAGgtacgacgcg ... ctatatgcagCTTCTTGGGCGAAGCGGCGGGTTTCAAGTGGCTTCAACACATCGGCCTTGCACCAAAGGACTTTGGATGTGGAGTGCGCCTTTGAAGAGAACTGGTCTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 141

CCCCGAGGCGGTGGCCGCGCTGCAGCTCGTCAAGGGCCCCGTCGGGGTCGTCTCCGTCTGCGGCCGCGCGCGCCAGGGCAAGAGCTTCATCCTCAACCAGgtacgacgcg ... ctatatgcagCTTCTTGGGCGAAGCGGCGGGTTTCAAGTGGCTTCAACACATCGGCCTTGCACCAAAGGACTTTGGATGTGGAGTGCGCCTTTGAAGAGAACTGGTCTGG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 111

CCCCGAGGCGGTGGCCGCGCTGCAGCTCGTCAAGGGCCCCGTCGGGGTCGTCTCCGTCTGCGGCCGCGCGCGCCAGGGCAAGAGCTTCATCCTCAACCAGgtacgacgcg ... ctatatgcagCTTCTTGGGCGAAGCGGCGGGTTTCAAGTGGCTTCAACACATCGGCCTTGCACCAAAGGACTTTGGATGTGGAGTGCGCCTTTGAAGAGAACTGGTCTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attattttttgttaatcctctgcatcagttgataaaatccatcctctatatgcagCTTCTTGGGCGAAGCGGCGGGTTTCAAGTGGCTTCAACACATCGGCCTTGCACCAAAGGACTTTGGATGTGGAGTGCGCCTTTGAAGAGAACTGGTCTGG
                                     tccatcctct  CT-rich tract
     tttttgttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatactcatactcagctttaatataagttgattttttatagtgcattattttttgttaatcctctgcatcagttgataaaatccatcctctatatgcagCTTCTTGGGCGAAGCGGCGGGTTTCAAGTGGCTTCAACACATCGGCCTTGCACCAAAGGACTTTGGATGTGGAGTGCGCCTTTGAAGAGAACTGGTCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
-catactc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatcct