Sequence
atgc intronic sequence ATGC exonic sequencegtatatataatatatccattcatcataacaaacactgattttccttggctcacacacacatgtcttttaattgttgacataatttataaaagacttgtacttcattgttatatttgattgtgaatcttcttcttgcaatgcagGTGTTGAATGACCAAGCATTTGCCATTTGTGTTCTCATGGCATTGTTTACCACCTTCATCACCACCCCAATAGTAATGGCTGTTTATAAACCAGCTCGCA
Basic information
species | Glycine max |
transcript | GLYMA17G04820.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G04820.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G17630.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatatataatatatccattcatcataacaaacactgattttccttggctcacacacacatgtcttttaattgttgacataatttataaaagacttgtacttcattgttatatttgattgtgaatcttcttcttgcaatgcagGTGTTGAATGACCAAGCATTTGCCATTTGTGTTCTCATGGCATTGTTTACCACCTTCATCACCACCCCAATAGTAATGGCTGTTTATAAACCAGCTCGCA
| | || |||| || | | | | |||||||| | || | | ||||| | || || || ||| | ||||||| ||||||| ||||||||||| || | || || ||||||||||| || ||||||||||| || ||||| || ||| | |||| || || || | |
-----------------------------------------------------gtatagat-tcttgaaagccataataagacttataaaacatttaaaagccga-gttat-ctaaataacga------tttttgtga-gcagGTGCTGAATGATCAAGCATTTGCGATCTTAGTCCTAATGGCATTGTTCACAACCTTCATCACAACTCCAATTGTGATGCTTATTTACAAGCCTGCAAGAA
upper sequence: GLYMA17G04820.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0020g01150.t01 (Vitis vinifera), 3'ss of exon 2
gtatatataatatatccattcatcataacaaacactgattttccttggctcacacacacatgtcttttaattgttgacataatttataaaagacttgtacttcattgttatatttgattgtgaatcttcttcttgcaatgcagGTGTTGAATGACCAAGCATTTGCCATTTGTGTTCTCATGGCATTGTTTACCACCTTCATCACCACCCCAATAGTAATGGCTGTTTATAAACCAGCTCGCA
| | | |||||| || | || || ||||| ||| | || | | | | || |||| || | | | | ||||| ||||||| || | ||||| || | ||||| ||||| ||||| ||||||||||||||||||||||| || | || | ||||| ||||| | |
---------------------------------------gtacataagctcactcattctggtac----atagttgatgatttttggtctgggtaggtggctgaccatcttgcttccttgt-----ttgattatata-tatagGTGCTGAATGATCAGACTTTTGCTATCTTAGTTCTTATGGCGTTGTTCACCACCTTCATCACCACCCCAATTGTGACCGCCTTGTATAAGCCAGCCAGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagacttgtacttcattgttatatttgattgtgaatcttcttcttgcaatgcagGTGTTGAATGACCAAGCATTTGCCATTTGTGTTCTCATGGCATTGTTTACCACCTTCATCACCACCCCAATAGTAATGGCTGTTTATAAACCAGCTCGCA
atttgat putative branch site (score: 5)
tcttcttcttgc putative PPT
attgttatatttgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatataatatatccattcatcataacaaacactgattttccttggctcacacacacatgtcttttaattgttgacataatttataaaagacttgtacttcattgttatatttgattgtgaatcttcttcttgcaatgcagGTGTTGAATGACCAAGCATTTGCCATTTGTGTTCTCATGGCATTGTTTACCACCTTCATCACCACCCCAATAGTAATGGCTGTTTATAAACCAGCTCGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC