Sequence
atgc intronic sequence ATGC exonic sequencegtataacatactttcctctgtaattttgtatgttcaataattttggatgttttgtttatgcagttgcattttaccaccttaattttttttttttttttaatttcacagCTAAAGTTTCCATCAGCACTTGCATCTTTTGATCAAATTACCAACTGTGCAAAAGGAAAGAGAATAGCATTGTTTCTGGATTATGATGGAACTCTTTCAC
Basic information
species | Glycine max |
transcript | GLYMA06G47630.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G47630.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G51460.2 (Arabidopsis thaliana), 3'ss of exon 1
gtataacatactttcctctgtaattttgtatgttcaataattttggatgttttgtttatgcagttgcattttaccaccttaattttttttttttttttaatttcacagCTAAAGTTTCCATCAGCACTTGCATCTTTTGATCAAATTACCAACTGTGCAAAAGGAAAGAGAATAGCATTGTTTCTGGATTATGATGGAACTCTTTCAC
|||| |||| | | | ||| | | ||| | || ||| | | || | || ||| |||| | | | ||| ||||| |||| ||||||||| ||| | |||||||| |||| | | | ||||||||| || ||||||||||||||||| |||||||| || || ||||| |
-----gtcagtcccttactgtcctttttttcatctgaaaatatgtgccgttgttttgatgttgatagtctt---ctttttgttttgttttataatcctgttttagcagCTCAAGTATCCATCAGCTCTTACCTCTTTTGAGAAAATCATGAGTTTTGCAAAAGGCAAAAGAATAGCATTGTTTCTTGATTATGACGGGACACTTTCGC
upper sequence: GLYMA06G47630.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G51460.1 (Arabidopsis thaliana), 3'ss of exon 2
gtataacatactttcctctgtaattttgtatgttcaataattttggatgttttgtttatgcagttgcattttaccaccttaattttttttttttttttaatttcacagCTAAAGTTTCCATCAGCACTTGCATCTTTTGATCAAATTACCAACTGTGCAAAAGGAAAGAGAATAGCATTGTTTCTGGATTATGATGGAACTCTTTCAC
|||| |||| | | | ||| | | ||| | || ||| | | || | || ||| |||| | | | ||| ||||| |||| ||||||||| ||| | |||||||| |||| | | | ||||||||| || ||||||||||||||||| |||||||| || || ||||
-----gtcagtcccttactgtcctttttttcatctgaaaatatgtgccgttgttttgatgttgatagtctt---ctttttgttttgttttataatcctgttttagCAGCTCAAGTATCCATCAGCTCTTACCTCTTTTGAGAAAATCATGAGTTTTGCAAAAGGCAAAAGAATAGCATTGTTTCTTGATTATGACGGGACACTTT---
upper sequence: GLYMA06G47630.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0022g00660.t01 (Vitis vinifera), 3'ss of exon 1
gtataacatactttcctctgtaattttgtatgttcaataattttggatgttttgtttatgcagttgcattttaccaccttaattttt----tttttttttttaatttcacagCTAAAGTTTCCATCAGCACTTGCATCTTTTGATCAAATTACCAACTGTGCAAAAGGAAAGAGAATAGCATTGTTTCTGGATTATGATGGAACTCTTTCAC
||| | | | ||| ||| || |||| || | || ||| | | | | || |||| || | | |||| || | |||| ||||| |||| ||||||||||||| ||||||||| ||||| || |||| ||| || ||||| |||||||||||||||||||| |||||||| ||||| ||||
gtaaattttgccc-cctttgtg-ttgtgtaactttggaggctc---atctttgatggaaccctagatggctgactgacttagttcctgccctcttttcttgtgattttgcagCTTAAGTATCCATCAGCACTTAAATCTTTTGAGCAAATCACGAACTATGCCAAGGGAAAAAGAATAGCATTGTTTCTGGACTATGATGGGACTCTCTCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttatgcagttgcattttaccaccttaattttttttttttttttaatttcacagCTAAAGTTTCCATCAGCACTTGCATCTTTTGATCAAATTACCAACTGTGCAAAAGGAAAGAGAATAGCATTGTTTCTGGATTATGATGGAACTCTTTCAC
ttttaat putative branch site (score: 3)
ccttaatttttttttt CT-rich tract
attttaccaccttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataacatactttcctctgtaattttgtatgttcaataattttggatgttttgtttatgcagttgcattttaccaccttaattttttttttttttttaatttcacagCTAAAGTTTCCATCAGCACTTGCATCTTTTGATCAAATTACCAACTGTGCAAAAGGAAAGAGAATAGCATTGTTTCTGGATTATGATGGAACTCTTTCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA