Sequence
atgc intronic sequence ATGC exonic sequencegtatgactaaatgaaaaactagttaaactaaacattatatagtttatcattacaattattaaagaatgaattgtgcttttaattgtgtgccttttcttgatccattggctatagATTCATTTTTTCCGTCCAGTTCCTAAGGAATATTTGCACTCAGCTGAGTTGAGAGACATAATGCAATTTGGAAGCAGTAATACTGCAGTCTTCTTTAAAA
Basic information
species | Glycine max |
transcript | GLYMA09G32740.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 9
gtatgactaaatgaaaaactagttaaactaaacattatatagtttatcattacaattattaaagaatgaattgtgcttttaattgtgtgccttttcttgatccat-tggctatagATTCATTTTTTCCGTCCAGTTCCTAAGGAATATTTGCACTCAGCTGAGTTGAGAGACATAATGCAATTTGGAAGCAGTAATACTGCAGTCTTCTTTAAAA
| | | | | ||| | || | | | | || | || | |||||| || | | || |||||||||||||||| ||||| ||||||||| | || || || || ||||||| || ||||||||||| ||||| ||||| || || ||||||||||
------------------------------------gtctgatgcctaaccacatgttgaaatgctatacgttttctgccagttttagctaatttctttttctgcgttaatgcagGTTCATTTTTTCCGTCCGGTTCCCAAGGAATATCTTCATTCTGCAGAACTGAGAGATATCATGCAATTTGGGAGCAGCAATACCGCTGTTTTCTTTAAAA
upper sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 10
gtatgactaaatgaaaaactagttaaactaaacattatatagtttatcattacaattattaaagaatgaattgtgcttttaattgtgtgccttttcttgatccattggctatagATTCATTTTTTCCGTCCAGTTCCTAAGGAATATTTGCACTCAGCTGAGTTGAGAGACATAATGCAATTTGGAAGCAGTAATACTGCAGTCTTCTTTAAAA
|| | || | | | | | || || ||| | |||| || || || ||| | || || || | || |||| ||||||||||||||||| ||||||||| | || || || || || |||||||| ||||||||||| ||||| |||||||| || ||||||||||
----------------gtctgatctcaccatgcgatggaaacttcat-attctttctgttaagtaa--aactgatcttgaatttatgca----------------tgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA
upper sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 9
gtatgactaaatgaaaaactagt-taaactaaacattatatagtttatcattacaattattaaagaatgaattgtgcttttaattgtgtgccttttcttgatccattggctatagATTCATTTTTTCCGTCCAGTTCCTAAGGAATATTTGCACTCAGCTGAGTTGAGAGACATAATGCAATTTGGAAGCAGTAATACTGCAGTCTTCTTTAAAA
|| | | || | | | | || || ||| | ||| || || || ||| | || || || | || |||| |||||||| || ||||| ||||||||| | || || || || | |||||||| ||||||||||| ||||| |||||||| |||||||||||||
----------------gtctgatctcgaccatgtaatggaagcttcat-attctttctgctaagtaa--aactgaccttgaatttctgca----------------tgaatgcagGTTCACTTTTTCCGCCCGGTTCCCAAGGAATATCTTCATTCTGCAGAACTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTCTTCTTTAAAA
upper sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G65930.1 (Arabidopsis thaliana), 3'ss of exon 8
gtatgactaaatgaaaaactagttaaactaaacattatatagtttatcattacaattattaaagaatgaattgtgcttttaattgtgtgccttttcttgatccattggctatagATTCATTTTTTCCGTCCAGTTCCTAAGGAATATTTGCACTCAGCTGAGTTGAGAGACATAATGCAATTTGGAAGCAGTAATACTGCAGTCTTCTTTAAAA
|| | || ||| ||| | | | || ||| | | | | ||| || | || | | || | || | || ||| ||| | || | ||| |||| ||||| || || |||||||| |||||| ||||||| ||||| | | ||||| ||||||||||| |||||||| ||||| ||||| || ||||
gttagtctcaatataaatgttatacattatgactttaaaaaaactgttattgttgtt-tggaattcaaatctatgttgttggatttgaa---tttgttgtttgctttcttgtagGTTCACTTTTTTCGACCGGTTCCTAAAGAATATCTGCACTCTGCTGAACTACGTGACATCATGCAATTTGGCAGCAGTAACACTGCTGTCTTTTTCAAAA
upper sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 10
gtatgactaaatgaaaaactagttaaactaaacattatatagtttatcattacaattattaaagaatgaattgtgcttttaattgtgtgccttttcttgatccattggctatagATTCATTTTTTCCGTCCAGTTCCTAAGGAATATTTGCACTCAGCTGAGTTGAGAGACATAATGCAATTTGGAAGCAGTAATACTGCAGTCTTCTTTAAAA
| | | | | ||| ||| | | || || | | || || || || || | || ||| ||| | |||| | || |||||||||||||||||||||| || || |||||||| || ||||| | ||||| |||||||||||||| ||||| |||||||| || || ||||| |
------gtgagtcagagttatattattataatgtatctgtacattgcaaatttgatgtttgaattatagatctattgcaacagaacatgaatttgattg-ttcattc-tcacagGTTCATTTTTTCCGTCCAGTTCCAAAAGAGTATTTGCATTCTGCTGAACTAAGAGATATAATGCAATTTGGTAGCAGCAATACTGCTGTATTTTTTAAGA
upper sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S364_50V6.1 (Physcomitrella patens), 3'ss of exon 12
----------------------------------------------------gtatgactaaatgaaaaactagttaaactaaacattatatagtttatcattacaattattaaagaatgaattgtgcttt---taattgtgtgccttttcttgatc-cattg----gctatagATTCATTTTTTCCGTCCAGTTCCTAAGGAATATTTGCACTCAGCTGAGTTGAGAGACATAATGCAATTTGGAAGCAGTAATACTGCAGTCTTCTTTAAAA
|||||| | || | ||| || || || | | ||||| | | | || || | ||| ||| ||| || || | || | || | ||||||||||| || || ||||| || |||||||| |||||||| || | ||||| ||||||||||| ||||| || || || ||||| || ||||
gtatgtgggagcgccttcatctttgtatgctttatcacttccataaacatttttatgaccagctgcgttgtgacgcttttccctcatatgttatttcatgactttgattatcgtggggtatagggtttttgacgttgttgcctgcatttattttgtcacgtttctgtattgcagGTGCATTTTTTCCGACCTGTGCCTAAAGAGTATTTGCATTCAGCTGAACTGCGCGACATTATGCAATTTGGTAGCAGCAACACAGCCGTCTTTTTCAAAA
upper sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ30174 (Selaginella moellendorffii), 3'ss of exon 10
gtatgactaaatgaaaaactagttaaactaaacattatatagtttatcattacaattattaaagaatgaattgtgcttttaattgtgtgccttttcttgatccat---tggctatagATTCATTTTTTCCGTCCAGTTCCTAAGGAATATTTGCACTCAGCTGAGTTGAGAGACATAATGCAATTTGGAAGCAGTAATACTGCAGTCTTCTTTAAAA
| || | || | ||| | | | |||| | | | || ||||||||||||| ||||| ||||| |||||||| || || |||||| |||||||||| |||||||||||||| || ||||| ||||| || |||||||
------------------------------------------------------------------gtacgtgcaagtatattcatgttcgctgttttgacatgtgtttcttaacagGTTCATTTTTTCCGGCCAGTACCTAAAGAATATTTACATTCGGCTGAGCTGAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAA
upper sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ06058 (Selaginella moellendorffii), 3'ss of exon 10
gtatgactaaatgaaaaactagttaaactaaacattatatagtttatcattacaattattaaagaatgaattgtgcttttaattgtgtgccttttcttgatccattggcta-tagATTCATTTTTTCCGTCCAGTTCCTAAGGAATATTTGCACTCAGCTGAGTTGAGAGACATAATGCAATTTGGAAGCAGTAATACTGCAGTCTTCTTTAAAA
| | | | || || || || ||| || || || || ||||||||||||| ||||| ||||| |||||||| || || |||||| | |||||||| |||||||||||||| || ||||| ||||| || |||||||
---------------------------------------------------------------gtacgtgcaagtatattcat-gttcgcggttttgacatgtgtttcttaacagGTTCATTTTTTCCGGCCAGTACCTAAAGAATATTTACATTCGGCTGAGCTTAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaagaatgaattgtgcttttaattgtgtgccttttcttgatccattggctatagATTCATTTTTTCCGTCCAGTTCCTAAGGAATATTTGCACTCAGCTGAGTTGAGAGACATAATGCAATTTGGAAGCAGTAATACTGCAGTCTTCTTTAAAA
ttttaattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgactaaatgaaaaactagttaaactaaacattatatagtttatcattacaattattaaagaatgaattgtgcttttaattgtgtgccttttcttgatccattggctatagATTCATTTTTTCCGTCCAGTTCCTAAGGAATATTTGCACTCAGCTGAGTTGAGAGACATAATGCAATTTGGAAGCAGTAATACTGCAGTCTTCTTTAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG