Sequence
atgc intronic sequence ATGC exonic sequencegtatcacaaccaatcactattccgtgtttctttcattcatttatggactcactgtgttaaccaaattatcttagAGGGATGACATTGAAGTGCTTGATGAGCCACTCTATGCTAATTTCCTTCGAGTCACTGCTGTTCATAGACCCTACAAGGAGGAACTACTCTCCAAAATG
Basic information
species | Glycine max |
transcript | GLYMA10G29770.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G29770.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g24460.2 (Oryza sativa), 3'ss of exon 1
----------------------------------------------------------------------------------------------------------------gtatcacaaccaatcactattccgtgtttc--tttcattcatttatggactcactgt--gttaaccaaattatcttagAGGGATGACATTGAAGTGCTTGATGAGCCACTCTATGCTAATTTCCTTCGAGTCACTGCTGTTCATAGACCCTACAAGGAGGAACTACTCTCCAAAATG
| || || || | || | | |||| | | ||| | | | || || |||||||||||||| || ||||| || ||||| ||||| ||||||||||| || ||||| | || | || || || ||||| || || || || |||
gtccgcgcctcctccttcgcctcgcctcggcctcgcccaccccgctgcgcacgggggatccccctgggccggcggcgagtcggcgaaccgggggccaccgccgcaaccagctgcattacctgcacggccggctcgcttcccccgtttcgctttctgatgattttttttttaattcttgtgtttgggatagAGGGATGACATGGAGGTGCTCGACGAGCCGCTCTACGCTAATTTCCTGCGCGTCACCGGCGTCGACAGGCCGTATCGCGAGGAGCTTCTGTCTAACATG
upper sequence: GLYMA10G29770.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G27410.2 (Arabidopsis thaliana), 3'ss of exon 11
---------gtatcacaaccaatcactattccgtgtttctttcattc-atttatgg-----------actcac----tgtgttaacc-aaattatcttagAGGGATGACATTGAAGTGCTTGATGAGCCACTCTATGCTAATTTCCTTCGAGTCACTGCTGTTCATAGACCCTACAAGGAGGAACTACTCTCCAAAATG
| || | | | || || | ||| | | | | || ||||| ||| | || || ||||| | |||| ||||||||||||||||||||||||||| | || ||| ||||| || | |||| |||| || ||||| || || || ||||| || |||
aacagttccgaataaaagttttttacatttttgagttattgtgaaactatgtatggtgtgagttgtaacttgcaagatgctttggtttaaatttcttcagAGAGATGACATTGAAGTGCTTGATGAGCCATTATACGCTGCGTTCCTCAAGTCTACGGGTGTTGATAGGCCTTACAAAGATGAGCTTCTCTCTAAGATG
upper sequence: GLYMA10G29770.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0128g00100.t01 (Vitis vinifera), 3'ss of exon 11
--------------------------------gtatcacaaccaatcactattccgtgtttctttcattcatttatggactcactgtgttaaccaaattatcttagAGGGATGACATTGAAGTGCTTGATGAGCCACTCTATGCTAATTTCCTTCGAGTCACTGCTGTTCATAGACCCTACAAGGAGGAACTACTCTCCAAAATG
|| | | | | | | | ||| ||| ||| || || ||| || ||| || || |||||||||| |||||||||||||||| || |||||||| ||||| ||||| || || | |||| | || |||||| ||||| || || ||||| |||
acttgaagccattatttgtgcatgtttctgagttacctctaaaattaattcctcctcgttaattttatgtccttttggttgtgctttgt------gttttcctcagAGGGATGATTTTGAAGTGCTTGATGAACCCCTCTATGCAAATTTTCTTCGGGTAACAGGTGTTGAAAGGCCCTACCGTGAGGAGCTTCTGTCCAAGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttccgtgtttctttcattcatttatggactcactgtgttaaccaaattatcttagAGGGATGACATTGAAGTGCTTGATGAGCCACTCTATGCTAATTTCCTTCGAGTCACTGCTGTTCATAGACCCTACAAGGAGGAACTACTCTCCAAAATG
tgttaac putative branch site (score: 2)
ttatctt putative PPT
tttcattcatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcacaaccaatcactattccgtgtttctttcattcatttatggactcactgtgttaaccaaattatcttagAGGGATGACATTGAAGTGCTTGATGAGCCACTCTATGCTAATTTCCTTCGAGTCACTGCTGTTCATAGACCCTACAAGGAGGAACTACTCTCCAAAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA