Sequence
atgc intronic sequence ATGC exonic sequencegtgcgtctctctatctttcatctccactatcattgccatgttcatttctcatttaattttttatgcatagGAATCGTCTCCGCTTGCTCACTCAATTCTTGGAGCATCTTGTAAGTGAAGGAAGCCAGGATGTACATGTACATAATGCCCTGGGTAAAATCATTATTGAC
Basic information
species | Glycine max |
transcript | GLYMA01G38580.1 |
intron # | 22 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 22
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 21
---------gtgcgtctctctatctttcatctccac-----tatcattgccatgttcatt---tctcatttaattttttatgcata---gGAATCGTCTCCGCTTGCTCACTCAATTCTTGGAGCATCTTGTAAGTGAAGGAAGCCAGGATGTACATGTACATAATGCCCTGGGTAAAATCATTATTGAC
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gtttgaattctttattcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctgtttgaatatgtgtatcagGAACCGCCTACGGTTGCTTACTCAATTCTTGGAGCATCTAGTGAGTGAAGGTAGCCAAGATGTGCATGTCCACAATGCTCTTGGGAAAATCATCATCGAC
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 22
lower sequence: GRMZM2G111355_T02 (Zea mays), 3'ss of exon 2
------------------------gtgcgtctctctatctttcatctccactatcattgccatgttcat----ttctcatttaattttttatgcatagGAATCGTCTCCGCTTGC-TCACTCAATTCTTGGAGCATCTTGTAAGTGAAG-GAAGCCAGGATGTACATGTACATAATGCCCTGGGTAAAATCATTATTGAC
| | | | || | | | | || ||||| ||| ||| | || | | || | || || | || | | | | ||| || | | | | | | | || ||| | | | | || | | | |||
gtttgtttttcatatcctcccagtttacttattcacatgagtgaaggtagccaagatgtgcatgtccataatgctcttggtaaaatcatcattgacagCAACAACAATCCTGAGCATTTCCTTACTACCAACCCATTTTACGACTCTCGTGTTGTGGGTAAATAT-TGTGAAAAGCGGGATCC-TACACTTGCTGTTGTT
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 22
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 22
---------------gtgcgtctctctatctttcatctccactatcattgccatgttcatttc-tcatttaattttttatgcatagGAATCGTCTCCGCTTGCTCACTCAATTCTTGGAGCATCTTGTAAGTGAAGGAAGCCAGGATGTACATGTACATAATGCCCTGGGTAAAATCATTATTGAC
|| || | | | || || | || || ||| ||| |||||| | |||| | || ||||||||||| || |||||||| ||||||||||||||||| ||||| || ||||||||||| ||||| |||||||| |||||||||||||| || |||
gtgcattgtttttacctgtgtaccgtttccattaatatttttaattcttattgctttcgttttatcattttgtgttttgtttgcagAAATCGTCTCCGTTTACTCACTCAGTTCTTGGAGCATCTTGTGAGTGAGGGTAGCCAGGATGTGCATGTTCATAATGCTCTGGGTAAAATCATCATAGAC
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 22
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 22
------------------------------gtgcgtctctctatctttcatctccactatcattgccatgttcatttctcatttaattttttatgcatagGAATCGTCTCCGCTTGCTCACTCAATTCTTGGAGCATCTTGTAAGTGAAGGAAGCCAGGATGTACATGTACATAATGCCCTGGGTAAAATCATTATTGAC
| | | | | | | | ||| | | || | || || | | | ||||||||||||| || || | || |||||||| |||||| | ||||||||||| ||||| ||||| ||||| || ||||| || || || ||||| || ||
atattagaactaggttgcgtttttaaatgtctaaacattttagtgtcacgatttaaacatcctgacgtcgtcgagaactgatgagttgtggggtttatagGAATCGTCTGCGACTGTTGACACAATTCTTAGAGCATTTGGTAAGTGAAGGTAGCCAAGATGTGCATGTGCACAATGCTCTTGGGAAGATCATCATAGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcatctccactatcattgccatgttcatttctcatttaattttttatgcatagGAATCGTCTCCGCTTGCTCACTCAATTCTTGGAGCATCTTGTAAGTGAAGGAAGCCAGGATGTACATGTACATAATGCCCTGGGTAAAATCATTATTGAC
atttaat putative branch site (score: 4)
ttttttat CT-rich tract
atgttcatttctcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcgtctctctatctttcatctccactatcattgccatgttcatttctcatttaattttttatgcatagGAATCGTCTCCGCTTGCTCACTCAATTCTTGGAGCATCTTGTAAGTGAAGGAAGCCAGGATGTACATGTACATAATGCCCTGGGTAAAATCATTATTGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG