Sequence
atgc intronic sequence ATGC exonic sequencegtgctttgtttttatttttacattgttgagaagaaactgtttacttatgtttttatttaaggttgtatgtatctatcgtgttacctgaaaaattggcaattctgagtttcttccttttcttgttgctcttatttgataaatatgcagGTCATGACTCCCAATTCAGTATGCGTAGTAATTGATACACCCATTGTTGATGCACTTCACACTATGCATGATGGAAAATTTTTGCATCTTCCTGCGGTTG
Basic information
species | Glycine max |
transcript | GLYMA06G17720.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G17720.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G133621_T01 (Zea mays), 3'ss of exon 4
gtgctttgtttttatttttacattgttgagaagaaactgtttacttatgtttttatttaaggttgtatgtatctatcgtgttacctgaaaaattggcaatt-ctgagtttcttccttttcttgttgctcttatttgataaatatgcagGTCATGACTCCCAATTCAGTATGCGTAGTAATTGATACACCCATTGTTGATGCACTTCACACTATGCATGATGGAAAATTTTTGCATCTTCCTGCGGTTG
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------------------------gcaagtcacataataattatctgtgtcattatgca--gtcacatttcattattctctaccttctcataatctcatcaactaacttacatcatgttc--ggaactcctttcca---------cagGTCATGACTCAGTGTCCTGAATGTGCCTCGGTAGACACCCCAATTCTTGATGCTCTTCACACAATGCATGATGGAAAATTTTTACATTTGCCTGTTCTGG
upper sequence: GLYMA06G17720.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G171622_T01 (Zea mays), 3'ss of exon 7
gtgctttgtttttatttttacattgttgagaagaaactgtttacttatgtttttatttaaggttgtatgtatctatcgtgttacctgaaaaattggcaattctgagtttcttccttttcttgttgctcttatttgataaatatgcagGTCATGACTCCCAATTCAGTATGCGTAGTAATTGATACACCCATTGTTGATGCACTTCACACTATGCATGATGGAAAATTTTTGCATCTTCCTGCGGTTG
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----------------------------------------gcaagtctctttacaattacctttgtatcgctatgcaatcacatttaattatctgtacctactcatcaactaactgccatcatgtttgaaattcctt---tccacagGTCATGACTCAGAGTCCTGAATGTGCCACAGTGGACACCCCAATTCTTGATGCTCTTCACACAATGCATGATGGGAAATTTTTACATTTGCCTGTCCTGG
upper sequence: GLYMA06G17720.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv17s0000g01200.t01 (Vitis vinifera), 3'ss of exon 8
----------------------------------gtgctttgtttttatttttacattgttgagaagaaactgtttacttatg--tttttatttaagg-ttgtatgt-atctatcgtgttacctgaaaaattggcaattctgagtttcttccttttcttgttgctcttatttgataaatatgcagGTCATGACTCCCAATTCAGTATGCGTAGTAATTGATACACCCATTGTTGATGCACTTCACACTATGCATGATGGAAAATTTTTGCATCTTCCTGCGGTTG
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gtatttgtctccagcctttctgtcaaaataaaatccaattcgttgtgtccttaaactttgctagaaatgattataaatgtgtcgcctattgtctgtgaattcttcatgataaactctcttatgaacaaaaaggataat----gacatttaactctgaatataactttt-tttatttcatgttcagGTCATGACTCCAAATCCAGAATGTGCAACAATTGATACACCCATTGTTGATGCCCTACATACCATGCATGATGGGAAATTTTTACACCTTCCTGTCATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggcaattctgagtttcttccttttcttgttgctcttatttgataaatatgcagGTCATGACTCCCAATTCAGTATGCGTAGTAATTGATACACCCATTGTTGATGCACTTCACACTATGCATGATGGAAAATTTTTGCATCTTCCTGCGGTTG
atttgat putative branch site (score: 5)
tcttatttgataaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgctttgtttttatttttacattgttgagaagaaactgtttacttatgtttttatttaaggttgtatgtatctatcgtgttacctgaaaaattggcaattctgagtttcttccttttcttgttgctcttatttgataaatatgcagGTCATGACTCCCAATTCAGTATGCGTAGTAATTGATACACCCATTGTTGATGCACTTCACACTATGCATGATGGAAAATTTTTGCATCTTCCTGCGGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA