Sequence
atgc intronic sequence ATGC exonic sequencegtaattcccattgttcttctcaaaaaacatagggtaatcataatgtgcatgtgctacaacaatatatgttcaaaaatgacctcaaaaagtgattgaactgtcattcaatttcagtaatctactcattttgtaattgcacaatccatggaattttatcctataaagttctttgcttcttcttagGTCCTAGAAGATGGAGTTCTTGATCCTGAGACTACCATAGTTGCCATATTTCCATCACCTATGCATTATGCTGGTCCAACTGAAGTACAGTGGCATGCAA
Basic information
species | Glycine max |
transcript | GLYMA13G06940.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G06940.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g02050.1 (Oryza sativa), 3'ss of exon 2
gtaattcccattgttcttctcaaaaaacatagggtaatcataatgtgcatgtgctacaacaatatatgttcaaaaatgacctcaaaaagtgattgaactgtcattcaatttcagtaatctactcattttgtaattgcacaatccatggaattttatcctataaagttctttgcttcttcttagGTCCTAGAAGATGGAGTTCTTGATCCTGAGACTACCATAGTTGCCATATTTCCATCACCTATGCATTATGCTGGTCCAACTGAAGTACAGTGGCATGCAA
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--------------------------------------------------------------------------------------------------------------gtaatcatttgtttatgcagttatttgctagttcaaactgtgcaaattactaaa----ttgatcatatggcagGTTTTAGAAGATGGTGTCCTTGATCCTGAGACTACTATAGTGTCTATTTTCCCCTCCCCGATGCATTATGCTGGTCCAACAGAAGTGCAATGGCATGCAA
upper sequence: GLYMA13G06940.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G158147_T01 (Zea mays), 3'ss of exon 2
gtaattcccattgttcttctcaaaaaacatagggtaatcataatgtgcatgtgctacaacaatatatgttcaaaaatgacctcaaaaagtgattgaactgtcat-tcaatttcagtaatctactcattttgtaattgcacaatccatggaattttatcctataaagttctttgcttcttcttagGTCCTAGAAGATGGAGTTCTTGATCCTGAGACTACCATAGTTGCCATATTTCCATCACCTATGCATTATGCTGGTCCAACTGAAGTACAGTGGCATGCAA
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----------------------------------------------------------------------------------------gt-atacatttgtcgtcttaatcttagctgtttaccggatgt---attatgcaaattgctgaagtttatcatgca------------------cagGTTTTAGAAGATGGAGTGCTTGATCCTGAGACTACTATAGTGTCTATATTTCCCTCACCAATGCATTATGCTGGTCCAACAGAAGTGCAGTGGCATGCAA
upper sequence: GLYMA13G06940.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G19920.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaattcccattgttcttctcaaaaaacatagggtaatcataatgtgcatgtgctacaacaatatatgttcaaaaatgacctcaaaaagtgattgaactgtcattcaatttcagtaatctactcattttgtaattgcacaatccatgg-aattttatcctataaagttctttgcttcttct---tagGTCCTAGAAGATGGAGTTCTTGATCCTGAGACTACCATAGTTGCCATATTTCCATCACCTATGCATTATGCTGGTCCAACTGAAGTACAGTGGCATGCAA
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------------------------------------------------------------------------------------------------gtgcatatttgctgttgtttccgagttcgttttcctcataaagaatttgttgtaaagagagattatgatttgatttgcttatgatgtgtagGTTCTAGAAGATGGAGTTCTTGACCCGAAGACTACTATTGTCTCGATCTTTCCGTCACCGATGCACTATGCTGGTCCAACTGAAGTTCAATGGCACGCCA
upper sequence: GLYMA13G06940.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g14010.t01 (Vitis vinifera), 3'ss of exon 2
gtaattcccattgttcttctcaaaaaacatagggtaatcataatgtgcatgtgctacaacaatatatgttcaaaaatgacctcaaaaagtgattgaactgtcattcaatttcagtaatctactcattttgtaattgcacaatccatggaattttatcctataaagttctttgcttcttcttagGTCCTAGAAGATGGAGTTCTTGATCCTGAGACTACCATAGTTGCCATATTTCCATCACCTATGCATTATGCTGGTCCAACTGAAGTACAGTGGCATGCAA
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--------------------------------------------------------------------------ttttatttta---gtcttttgacaagtttatgaaacttaaaaatttaattgtcatgtg-ttgtccaa--agttcaattttcttattcaaa---ttttatttttggacagGTCCTAGAAGATGGAGTCCTTGATCCTGAAACTACCATTGTGGCTATATTCCCATCACCTATGCATTATGCAGGCCCAACTGAAGTACAATGGCATGCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtaattgcacaatccatggaattttatcctataaagttctttgcttcttcttagGTCCTAGAAGATGGAGTTCTTGATCCTGAGACTACCATAGTTGCCATATTTCCATCACCTATGCATTATGCTGGTCCAACTGAAGTACAGTGGCATGCAA
ttctttgcttcttctt CT-rich tract
aattttatcctataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattcccattgttcttctcaaaaaacatagggtaatcataatgtgcatgtgctacaacaatatatgttcaaaaatgacctcaaaaagtgattgaactgtcattcaatttcagtaatctactcattttgtaattgcacaatccatggaattttatcctataaagttctttgcttcttcttagGTCCTAGAAGATGGAGTTCTTGATCCTGAGACTACCATAGTTGCCATATTTCCATCACCTATGCATTATGCTGGTCCAACTGAAGTACAGTGGCATGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG