Sequence
atgc intronic sequence ATGC exonic sequence...agcctttatgttattatgctaacatgatgtaaaacctcaccttatgctttttccatgcttcctttcattttatgcatgttgatacaagtttaacatgcagGGAAAATTGCCAAGATAAAATGGATCAGTTCTTAAAAAGATGCTTTTACCATTCTGGTCAATACAACTCCGAGGACCACTTTTCTGAATTGGGTAGCAAG
Basic information
species | Glycine max |
transcript | GLYMA08G21270.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G21270.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G35790.1 (Arabidopsis thaliana), 3'ss of exon 2
agcctttatgttattatgctaacatgatgtaaaacctcaccttatgctttttccatgcttcctttcattttatgcatgttgatacaagttt-aacatgcagGGAAAATTGCCAAGATAAAATGGATCAGTTCTTAAAAAGATGCTTTTACCATTCTGGTCAATACAACTCCGAGGACCACTTTTCTGAATTGGGTAGCAAG
| || || | || | | |||| ||| | | || ||| || | | | ||||| || ||||||||| || ||||| ||||| |||||||| |||||||||||||||||||| ||||| || ||||| || || | ||| | ||| | | |||
---------------gta-tattctgctatacgtttttagtgtatgttttagttaaagt---ttatgctttggttatatgaacaaaagttggaatcaacagGGAAAAATGTGGGGATAAGATGGAGCAGTTCTTGAAAAGATGCTTTTACCATTCGGGTCAGTATAACTCGGAAGAGGATTTTGCGGAACTAAACAAGAAG
upper sequence: GLYMA08G21270.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0057g00940.t01 (Vitis vinifera), 3'ss of exon 3
agcctttatgttattatgctaa-catgatgtaaaacctcaccttatgctttttccatgcttcctttcattttatgcatgttgatacaagtttaaca--tgcagGGAAAATTGCCAAGATAAAATGGATCAGTTCTTAAAAAGATGCTTTTACCATTCTGGTCAATACAACTCCGAGGACCACTTTTCTGAATTGGGTAGCAAG
| | |||| |||||| || | | | | ||| || | | | ||||||| |||| ||| ||| || ||| | || | ||||| | |||||| || || ||||| ||||||||||||||||||||||||||||| ||||| |||| ||| ||||| || ||| | ||||||| | |||
-----gtgttctattttgctaaacaatctctcatatgtcatatt-taatctaaccatgct---tttcttttcatgttcattaatatgtggagaaaacttgcagTGCAAATTGTGGTGACAAGATGGACCAGTTCTTAAAAAGATGCTTTTACCATTCGGGTCAGTACAGCTCTGAGGAGCATTTTGCAGAATTGGACAAGAAG
upper sequence: GLYMA08G21270.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0057g01030.t01 (Vitis vinifera), 3'ss of exon 3
agcctttatgttattatgctaacatgatgtaaaacctcaccttatgct--ttttccatgcttcctttcattttatgcatgttgatacaagtttaacat-gcagGGAAAATTGCCAAGATAAAATGGATCAGTTCTTAAAAAGATGCTTTTACCATTCTGGTCAATACAACTCCGAGGACCACTTTTCTGAATTGGGTAGCAAG
| ||| | | | ||| || | |||| ||| | ||||| | || | | | ||| || | ||| ||||||| | || |||||||||||||||||| | |||||||| || ||||||||||| |||| || ||||| || || || |||||| | |||
----------gtgccatgttc---ttttctaagctctactccattgctggtttactatgctctcaatctgcattgactaacaatccctagtgaggaattgtagGAAAAATTGTAACGAGAAAATGGATCAGTTCTTACAGAGATGCTTCTATCATTCTGGTCAGTACAGTTCTGAGGATCATTTCTCCAAATTGGACAAGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctttttccatgcttcctttcattttatgcatgttgatacaagtttaacatgcagGGAAAATTGCCAAGATAAAATGGATCAGTTCTTAAAAAGATGCTTTTACCATTCTGGTCAATACAACTCCGAGGACCACTTTTCTGAATTGGGTAGCAAG
gtttaac putative branch site (score: 3)
tttcattttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agcctttatgttattatgctaacatgatgtaaaacctcaccttatgctttttccatgcttcctttcattttatgcatgttgatacaagtttaacatgcagGGAAAATTGCCAAGATAAAATGGATCAGTTCTTAAAAAGATGCTTTTACCATTCTGGTCAATACAACTCCGAGGACCACTTTTCTGAATTGGGTAGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
-gccttta
- - - - - - - - tgctaac
- - - - - - - - - - - - tgatgta
- - - - - - - - - - - - - - - - - cctcacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgtt