Sequence
atgc intronic sequence ATGC exonic sequencegtttgtctcacaaatgactccccccccccccccccccccccctcttttcatctcagatacagactaattacttgtctaacaagccaacctgtaactaggggggaggaacttactaagtttccatggttgagcagGGTTATCGAGTTCTTGTTGTAGAGCAGACTGATACACCTGAACAGCTGGAGCTTCGTCGCAAGGAGAAGGGCTCTAAAGATAAG
Basic information
species | Glycine max |
transcript | GLYMA19G40350.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G40350.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os09g24220.1 (Oryza sativa), 3'ss of exon 6
gtttgtctcacaaatgactccccccccccccccccccccccctcttttcatctcagatacagactaattacttgtctaacaagccaacctgtaactaggggggaggaacttactaagtttccatggttgagcagGGTTATCGAGTTCTTGTTGTAGAGCAGACTGATACACCTGAACAGCTGGAGCTTCGTCGCAAGGAGAAGGGCTCTAAAGATAAG
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-----------------------------------------gtcagatcatgtttgatatgattttatt-cttccatggaaaataattacattttta------ataagctaacagagttg--gttgcatcacagGGTTATCGAGTTCTGGTTATCGAGCAGACTGAAACACCGGAGCAGCTTGACCTCCGCCGTAAAGAAACTGGTGTAAAAGACAAG
upper sequence: GLYMA19G40350.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G421541_T02 (Zea mays), 3'ss of exon 6
gtttgtctcacaaatgactccccccccccccccccccccccctcttttcatctcagatacagactaattacttgtctaacaagccaacctgtaactaggggggaggaacttactaa--gtttccatggttgagcagGGTTATCGAGTTCTTGTTGTAGAGCAGACTGATACACCTGAACAGCTGGAGCTTCGTCGCAAGGAGAAGGGCTCTAAAGATAAG
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----------------------------------------------------------gtaaacttatttaatgtttttcctcattaaatttcac-acataattgcattttagcaataacattaattgcattacagGGTTATCGAGTTCTGGTTGTCGAGCAAACTGAAACACCTGACCAGCTTGAACTTCGGCGTAAGGAGATGGGTATAAAGGACAAG
upper sequence: GLYMA19G40350.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0005g01370.t01 (Vitis vinifera), 3'ss of exon 6
gtttgtctcacaaatgactccccccccccccccccccccccctcttttcatctcagatacagactaattacttgtctaacaagccaacctgtaactaggggggaggaacttactaagtttccatggttga-gcagGGTTATCGAGTTCTTGTTGTAGAGCAGACTGATACACCTGAACAGCTGGAGCTTCGTCGCAAGGAGAAGGGCTCTAAAGATAAG
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gttgatcctattacatattttctatctcaaattagaattgttttccattggctt---tagagcacctctatttctttcatgaacccattttcatcaagaatt------cttactggagctccttggacagtgcagGGTTATCGTGTTCTTGTTGTAGAGCAAACAGAAACACCTGAGCAGCTTGAGCTTCGTCGCAAAGAGAAGGGTTCTAAGGACAAG
upper sequence: GLYMA19G40350.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S152_6V6.1 (Physcomitrella patens), 3'ss of exon 6
gtttgtctcacaaatgactccccccccccccccccccccccctcttttcatctcagatacagactaattacttgtctaacaagccaacctgtaactaggggggaggaacttactaagtttccatggttgagcagGGTTATCGAGTTCTTGTTGTAGAGCAGACTGATACACCTGAACAGCTGGAGCTTCGTCGCAAGGAGAAGGGCTCTAAAGATAAG
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-------ttactaatgtttggcgcatctctacaagcctcgagtcttggactgtacctggttggctcaatcctagtatact-------tctgtaatt-----------------taaatcttcatgtt---gcagGGATATCGAGTTCTTGTTGTGGAGCAGACAGAGACACCTGATCAGCTGGAAAAACGACGGAAAGAAACTGGTTCAAAGGATAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caagccaacctgtaactaggggggaggaacttactaagtttccatggttgagcagGGTTATCGAGTTCTTGTTGTAGAGCAGACTGATACACCTGAACAGCTGGAGCTTCGTCGCAAGGAGAAGGGCTCTAAAGATAAG
aacttac putative branch site (score: 2)
ttactaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtctcacaaatgactccccccccccccccccccccccctcttttcatctcagatacagactaattacttgtctaacaagccaacctgtaactaggggggaggaacttactaagtttccatggttgagcagGGTTATCGAGTTCTTGTTGTAGAGCAGACTGATACACCTGAACAGCTGGAGCTTCGTCGCAAGGAGAAGGGCTCTAAAGATAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA