Sequence
atgc intronic sequence ATGC exonic sequencegtaaagcccaattctggacattgtattgtagtgatggttttttctatatgccaatatgtgaatttgtttcctaatgtgcggagtgtgaacttcttgctagctggagcatacgttatttttgtcaagaattcttgatacattatgcaaaactctgcattgagccacttgaacttgtgttatcaacagGTGCTATGGCAATTGCAGTGGCAAATCCAACTGATCTTGTGAAAGTTAGACTTCAAGCAGAAGGAAAATTGCCTCCTGGCGTGCCCAAGCGCTACTCTGG
Basic information
species | Glycine max |
transcript | GLYMA07G17380.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G17380.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g74640.3 (Oryza sativa), 3'ss of exon 3
gtaaa-gcccaattctggacattgtattgtagtgatggttttttctatatgccaatatgtgaatttgtttcctaatgtgcggagtgtgaacttcttgctagctggagcatacgttatttttgtcaagaattc----ttgatacattatgcaaaactctgcattgagccacttgaacttgtgtt------atcaacagGTGCTATGGCAATTGCAGTGGCAAATCCAACTGATCTTGTGAAAGTTAGACTTCAAGCAGAAGGAAAATTGCCTCCTGGCGTGCCCAAGCGCTACTCTGG---
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gtgggtacttttccctatccgtttctctttgctgcactttctcaataatttgtcacatattaaattgcttt------tgctaattaaatgcagccaaccagtttacatccaaatttcatgtgttaaggacttaaggtaggtgcactatgcacaagtaaatatactcttatattaattaccgttctatatattcatagGTGTCATAGCAATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTGAGATTGCAAGCTGATGGAAAGGCCACCACTGTCAAG---AGGCACTATTCTGGAGC
upper sequence: GLYMA07G17380.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G165629_T02 (Zea mays), 3'ss of exon 3
gtaaagcccaattctggacattgtattgtagtgatggttttttctatatgccaatatgtgaatttgtttcctaatgtgcggagtgtgaacttcttgctagctggagcatacgttatttttgtcaagaattcttgat--acattatgcaaaactctgcattgagccacttgaacttgtgttatcaa----cagGTGCTATGGCAATTGCAGTGGCAAATCCAACTGATCTTGTGAAAGTTAGACTTCAAGCAGAAGGAAAATTGCCTCCTGGCGTGCCCAAGCGCTACTCTGG---
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------------------------------------------------------------------------------------------tcatagataataaaatcaggtcggttcactttaaaggtgccacgctcggcaatgtggagaaccatacattg--ttaaatgatctttttttgtctattttcagGTGTGATAGCAATTGTTGTGGCAAATCCAACTGATCTTGTTAAAGTTAGGTTGCAAGCTGATGGAAAGGCTAACACTGTCAAG---AGGAGTTATTCTGGAGC
upper sequence: GLYMA07G17380.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G852877_T01 (Zea mays), 3'ss of exon 3
gtaaagcccaattctggacattgtattgtagtgatggttttttctatatgccaatatgtgaatttgtttcctaatgtgcggagtgtgaacttcttgctagctggagcatacgttatttttgtcaagaattcttgat--acattatgcaaaactctgcattgagccacttgaacttgtgttatcaa----cagGTGCTATGGCAATTGCAGTGGCAAATCCAACTGATCTTGTGAAAGTTAGACTTCAAGCAGAAGGAAAATTGCCTCCTGGCGTGCCCAAGCGCTACTCTGG---
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------------------------------------------------------------------------------------------atcgcagttaataaatcaggtcggttcactttaaaggtgccacactcagcaatgtggagaaccatacattg--ttaaatgatctttttttgtctattctcagGTGTGATAGCGATTGTTGTGGCAAATCCAACTGATCTTGTCAAAGTTAGGTTGCAAGCTGATGGAAAAGCTAACACTATCAAG---AGGAGTTATTCTGGAGC
upper sequence: GLYMA07G17380.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0007g01700.t01 (Vitis vinifera), 3'ss of exon 3
gtaaagcccaattctggacattgtattgtagtgatggttttttctatatgccaatatgtgaatttgtttcctaatgtgcggagtgtgaacttcttgctagctggagcatacgttatttttgtcaagaattcttgatacattatgcaaaactctgcattgagccacttgaacttgtgttatcaa-cagGTGCTATGGCAATTGCAGTGGCAAATCCAACTGATCTTGTGAAAGTTAGACTTCAAGCAGAAGGAAAATTGCCTCCTGGCGTGCCCAAGCGCTACTCTGG
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------------------------------gtgagcacatatgctggactctgatgt----acttgtttt-tcatttgaatataatgag--tatggtgagc--acatactcatgattcctattaa--acttgtgat-tgggatttaattctc-atgatgtacttgtttaattctcataattaaacagGTGGTCTAGCGATTACAATTGCCAATCCAACTGACCTTGTGAAAGTTCGACTTCAATCTGAAGGAAAATTGCCACCTGGTGTGCCAAGACGCTATTCCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgatacattatgcaaaactctgcattgagccacttgaacttgtgttatcaacagGTGCTATGGCAATTGCAGTGGCAAATCCAACTGATCTTGTGAAAGTTAGACTTCAAGCAGAAGGAAAATTGCCTCCTGGCGTGCCCAAGCGCTACTCTGG
tcttgat putative branch site (score: 4)
acattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagcccaattctggacattgtattgtagtgatggttttttctatatgccaatatgtgaatttgtttcctaatgtgcggagtgtgaacttcttgctagctggagcatacgttatttttgtcaagaattcttgatacattatgcaaaactctgcattgagccacttgaacttgtgttatcaacagGTGCTATGGCAATTGCAGTGGCAAATCCAACTGATCTTGTGAAAGTTAGACTTCAAGCAGAAGGAAAATTGCCTCCTGGCGTGCCCAAGCGCTACTCTGG
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