Sequence
atgc intronic sequence ATGC exonic sequence...tttagttctaaattcttataacattgatgctgctagttatagtgtatgaatgcattattgataactatgatttgaaacctgtcctactatttctttgcagGAGTTCAGTGGTAGGGTCAAGGGGTTAAAGGTGGATGCTGTTGACACCACTGGTGCTGGTGATGCATTTGTGGCTGGAATATTATCACAATTAGCTGTGG
Basic information
species | Glycine max |
transcript | GLYMA02G41320.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G41320.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g12600.1 (Oryza sativa), 3'ss of exon 5
--tttagttctaaattcttataacattgatgctgctagttatagtgta-tgaatgcattattgataactatgatttgaaacctgtcctactatttctttgcagGAGTTCAGTGGTAGGGTCAAGGGGTTAAAGGTGGATGCTGTTGACACCACTGGTGCTGGTGATGCATTTGTGGCTGGAATATTATCACAATTAGCTGTGG
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actatctcgtttattttttcttgcagtcacttggaaccttattgtgtaactaaggctgtataaattgtgcctaatgttaatgtttcttgtaaaata---acagGAATTTAATGGGAGAGTTGGTGGACTTAAGGTGAATGCTGTTGACACCACTGGTGCTGGAGATGCCTTTGTTGCTGGAATACTATCCCAGCTATCTGTTG
upper sequence: GLYMA02G41320.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G072091_T01 (Zea mays), 3'ss of exon 5
---tttagttctaaattcttataacattgatgctgctagttatagtgtatgaatgcattattgataactatgatttgaaacctgtcctactatttctttgcagGAGTTCAGTGGTAGGGTCAAGGGGTTAAAGGTGGATGCTGTTGACACCACTGGTGCTGGTGATGCATTTGTGGCTGGAATATTATCACAATTAGCTGTGG
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caaacttttcttaaatcttaactacatttac-ttgctaacaatgccttatgcacataggtctgtaaaatgttgtttacagtacatttt--tgtggaataacagGATTTTAGTGGTAGAGTTGGTGGACTTAAGGTAAGTGCTGTTGACACAACTGGTGCTGGCGATGCCTTTGTTGCTGGAGTGCTATCTCAATTAGCCACAG
upper sequence: GLYMA02G41320.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0006g01410.t01 (Vitis vinifera), 3'ss of exon 5
tttagttctaaattcttataacattgatgctgctagttatagtgtatgaatgcattattgataactatga-tttgaaacc---tgtcctactatttctttgcagGAGTTCAGTGGTAGGGTCAAGGGGTTAAAGGTGGATGCTGTTGACACCACTGGTGCTGGTGATGCATTTGTGGCTGGAATATTATCACAATTAGCTGTGG
| || || | ||| | || ||| | ||| | || | | | | | | ||| ||||| || | || | | | | ||||| |||||||| || || || || ||||| |||||||| || |||||||| || ||||| ||||| ||||| |||||||||||||||||| |||||| |
-gaatttttagacccttg---cttttttgcaagcaattacaatgatgcagtctgtcttctgagattgtgaacctgaaattgcatgggatgctttatttgttcagGACTTCAGTGGGAGAGTTAAAGGTTTAAAAGTGGATGCAGTGGACACCACAGGCGCTGGGGATGCTTTTGTTGCTGGAATATTATCACAACTAGCTGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgaatgcattattgataactatgatttgaaacctgtcctactatttctttgcagGAGTTCAGTGGTAGGGTCAAGGGGTTAAAGGTGGATGCTGTTGACACCACTGGTGCTGGTGATGCATTTGTGGCTGGAATATTATCACAATTAGCTGTGG
tgataac putative branch site (score: 2)
tcctactatttcttt putative PPT
attattgataactat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttagttctaaattcttataacattgatgctgctagttatagtgtatgaatgcattattgataactatgatttgaaacctgtcctactatttctttgcagGAGTTCAGTGGTAGGGTCAAGGGGTTAAAGGTGGATGCTGTTGACACCACTGGTGCTGGTGATGCATTTGTGGCTGGAATATTATCACAATTAGCTGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - atgctgc
- - - - - - - - - - - - - - - - - - - - - - - -gaatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatttg