Sequence
atgc intronic sequence ATGC exonic sequencegtctgttattaactatttacaaaatttaaatgatcattcaaaattacaatccaaagtaagagaatggttacttgctactcaggaatattcatttctatattttctcccaccttttttttatttttcccttaattttccttaaatatacttttagATGGGAGGAAGGAACACAGTACTTTTGGATGCGCTAAGTTGGAGAATCCCATTGGTTAGTGACATTCCAACAATAATTTTTGGAGCAGATGTAACTCATC
Basic information
species | Glycine max |
transcript | GLYMA05G08170.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G08170.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 13
gtctgttattaactatttacaaaatttaaatgatcattcaaaattacaatccaaagtaagagaatggttacttgctactcaggaatattcatttctatattttctcccaccttttttttatttttcccttaattttccttaaatatacttttagATGGGAGGAAGGAACACAGTACTTTTGGATGCGCTAAGTTGGAGAATCCCATTGGTTAGTGACATTCCAACAATAATTTTTGGAGCAGATGTAACTCATC
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--------------------------------gtaccaaatacttataaaccaagc--agttaatacttagcttgtctacacaaatgtagtgtaatgcagtaagcagacttgcagcattgctaatgccttgcatttcg--gagttgtgatacagATGGGAGGAAGAAACACCGTGCTGCTGGATGCAATAAGTTGGAGGATTCCTTTGGTCAGTGACATACCAACTATTATATTTGGTGCAGATGTCACGCATC
upper sequence: GLYMA05G08170.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 13
gtctgttattaactatttacaaaatttaaatgatcattcaaaattacaatccaaagtaagagaatggttacttgctactcaggaatattcatttctatattttctcccacct---tttttttatttttcccttaattttccttaaatatacttttagATGGGAGGAAGGAACACAGTACTTTTGGATGCGCTAAGTTGGAGAATCCCATTGGTTAGTGACATTCCAACAATAATTTTTGGAGCAGATGTAACTCATC
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-----------------------------------------------------------gtacttaccaccttgtttatacataaaatacagtt-tagaacatcaactatataagtggctctattattgactaatggtacc---aataaaattc-agATGGGAGGAAGAAACACTGTGCTCCTGGACGCAATAAGTTGGAGGATTCCGTTGGTCAGTGACATCCCAACTATTATATTTGGTGCAGATGTAACACATC
upper sequence: GLYMA05G08170.1 (Glycine max), 3'ss of exon 12
lower sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 12
gtctgttattaactatttacaaaatttaaatgatcattcaaaattacaatccaaagtaagagaatggttacttgctactcagga---atattcatttctatattttctcccaccttttttttatttttcccttaattttccttaaatatact------tttagATGGGAGGAAGGAACACAGTACTTTTGGATGCGCTAAGTTGGAGAATCCCATTGGTTAGTGACATTCCAACAATAATTTTTGGAGCAGATGTAACTCATC
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-------------------------------------------------------------------gtacttaccaccttggttatacatcaaatacagttcagaacagcaactttataagagaaatggctcgatattgactaatgataccatcaaattcagATGGGAGGAAGAAACACTGTGCTCCTGGACGCAATAAGTTGGAGCATTCCTTTGGTCAGTGACATCCCAACTATTATATTTGGTGCAGATGTAACACACC
upper sequence: GLYMA05G08170.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 13
gtctgttattaactatttacaaaatttaaatgatcattcaaaattacaatccaaagtaagagaatggttacttgctactcaggaatattcatttctatattttctcccaccttttttttatttttcccttaattttccttaaatatacttttagATGGGAGGAAGGAACACAGTACTTTTGGATGCGCTAAGTTGGAGAATCCCATTGGTTAGTGACATTCCAACAATAATTTTTGGAGCAGATGTAACTCATC
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-------------------------------gtctgtccagactgaaacttct--gtggcgattctactacttaaaaat--agattgcttattgcaaagttaatgtttcctctaagcttggttt---cgggatttttctt-----tttccccagATGGGTGGAAGAAATACTGTGCTTTTAGATGCTTTGAGTTCAGGAATTCCTTTGGTTAGTGACATTCCAACAATCATATTTGGAGCCGATGTAACTCATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttctcccaccttttttttatttttcccttaattttccttaaatatacttttagATGGGAGGAAGGAACACAGTACTTTTGGATGCGCTAAGTTGGAGAATCCCATTGGTTAGTGACATTCCAACAATAATTTTTGGAGCAGATGTAACTCATC
ccttaat putative branch site (score: 4)
tactttt putative PPT
ttttttttatttttcc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgttattaactatttacaaaatttaaatgatcattcaaaattacaatccaaagtaagagaatggttacttgctactcaggaatattcatttctatattttctcccaccttttttttatttttcccttaattttccttaaatatacttttagATGGGAGGAAGGAACACAGTACTTTTGGATGCGCTAAGTTGGAGAATCCCATTGGTTAGTGACATTCCAACAATAATTTTTGGAGCAGATGTAACTCATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG