Sequence
atgc intronic sequence ATGC exonic sequencegtgagaaaattaaaagcatacgtgttttttgagttattgtctactgttgtagttttattcttccataatgtattttttttgtttgtttgttttggtttcaaacagGGTGAAGCACAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCTGAAACTGCTGAGCTTGTTACACG
Basic information
species | Glycine max |
transcript | GLYMA05G30530.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g51480.1 (Oryza sativa), 3'ss of exon 3
gtgagaaaattaaaagcatacgtgttttttgagttattgtctactgttgtagttttattcttccataatgtattttttttgtttgtttgttttggtttcaaacagGGTGAAGCACAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCTGAAACTGCTGAGCTTGTTACACG
|| || |||| ||| |||| | || || | ||||||| | | || | | | ||| | | | | || ||| ||| | ||||| | ||||| ||||| |||||||||||||||||||||||||| || |||||| |||| | |||||| | || |
gtcagccaatt-------tac-tgttcctcgacttgccatt--ctgttgttgccgtgcactggatggtaaaactaacactatttatct--tacgccttt---cagAATGAGACTCAGGACTTCCTTTTCATTGCGACTGAAAGATACAAATTCTGTGTTCTGCAGTGGGATGGAGAAAAATCGGAGCTTCTCACTAG
upper sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g51480.2 (Oryza sativa), 3'ss of exon 3
gtgagaaaattaaaagcatacgtgttttttgagttattgtctactgttgtagttttattcttccataatgtattttttttgtttgtttgttttggtttcaaacagGGTGAAGCACAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCTGAAACTGCTGAGCTTGTTACACG
||| | | ||| | || | ||| ||| | ||||| | ||||| ||||| |||||||||||||||||||||||||| || |||||| |||| | |||||| | || |
---------------------------------------------------------------------gtaaaactaacact-atttatctta-cgcctttcagaatgagactcaggacttccttttcattgcgactgaaagatacaaattctgtgttctgcagTGGGATGGAGAAAAATCGGAGCTTCTCACTAG
upper sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 3
gtgagaaaattaaaagcatacgtgttttttgagttattgtctactgttgtagttttattcttccataatgtattttttttgtttgtttgttttggtttcaaacagGGTGAAGCACAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCTGAAACTGCTGAGCTTGTTACACG
|| || |||| |||| | | | || | | | |||| | ||| || | |||| ||||||| ||||||||| || | | ||| ||| | ||||| | |||||| ||||| || || || ||||||||||||||||| ||||||||| | |||| | ||||| | || |
gtaagctaatttaaagttcatccatccgagatact-ttatttgtttttgtgaagt-atttttata-aatggattttttctgtttgtttcttatcct------cagAATGAGACTCAGGACTTTCTTTTCATTGCTACGGAGAGGTACAAATTCTGTGTTCTGCAATGGGATGCAGAAAAGTCAGAGCTAATCACCAG
upper sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagaaaattaaaagcatacgtgttttttgagttattgtctactgttgtagttttattcttccataatgtattttttttgtttgtttgttttggtttcaaacagGGTGAAGCACAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCTGAAACTGCTGAGCTTGTTACACG
|| ||| | | || | || | | |||| | | || | | ||| || || ||| | | | | ||| |||||||||||||| || | | | ||| |||||||||||||||| ||||||||||||||||||||||||| ||| | |||||||| ||||| |
-----------gtgagtatagttttcttattgaatacttttctctgtc-tgaggtaatacgtaagtaaca-atgttaattgatagcacttcatctttt---gcagGGTGAAGCACAAGACTTTTTGTTTGTTGCAACTGAAAGATATAAATTCTGTGTTCTTCAATGGGATTATGAGTCCTCTGAGCTTATTACAAG
upper sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagaaaattaaaagcatacgtgttttttgagttattgtctactgttgtagttttattcttccataatgtattttttttgt-ttgtttgttttggtttcaaacagGGTGAAGCACAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCTGAAACTGCTGAGCTTGTTACACG
| || | | | || || | ||| ||| | || ||| | | | | || || | || |||| | ||| |||| ||||| || || | | | || ||||||||||| |||||||||||||||||||||||||||||| |||| | |||||||| ||||| |
-------------gtgagtatatatctctta--ttgtgttcttttgtcatggtcttaataatgagttaaa-atgttgatagtattgtccaccgtctttt---gtagGGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAG
upper sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 3'ss of exon 3
gtgagaaaattaaaagcatacgtgttttttgag--ttattgtctactgttgtagttttattcttccataatgtattttttttgtttgtttgttttggtttcaaacagGGTGAAGCACAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCTGAAACTGCTGAGCTTGTTACACG
|| || | | | | | | | ||| | || || || | | | || || || | | ||| ||| | ||||||| ||| ||||||| |||||||| |||| ||| || || ||||||||||||||||| || |||||||||||||||||| | || | | ||||| || ||||| |
-----gtaagtatcatcttgtgacatatagaaagcttacttagtagcattataatcatgctttt---tatgctaatactattgcttgct-gttttggattctaacagGGCGAAGCACAAGATTTTCTATTCATCGCAACTGAAAGATACAAGTTTTGTGTTCTTCAATGGGATGCAGAGAATTCTGAGGTTATTACAAG
upper sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S203_55V6.1 (Physcomitrella patens), 3'ss of exon 3
gtgagaaaattaaaagcatacgtgttttttgagttattgtctactgttgtagttttattcttccataatgtattttttttgtttgtttgttttggtttcaaacagGGTGAAGCACAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCTGAAACTGCTGAGCTTGTTACACG
| | | | | || | || | ||| | | || || | | | ||| || | | |||| ||||||||| |||| || || ||||| | |||||||| ||||| |||||||||||||||||| | ||||| | | | |||||||
----ggttccttatcgtacttgtcaacatggaactcagcgctagcatatgaacttataaaaaatatgacgcaacgaaaac-tttattgttgtgcttttcttacagGGTGAGTCACAAGACGTGCTATTTATATCGTTCGAAAGATATAAATTTTGTGTTCTTCAATGGGATGCAGAAACCGGCTCACCTATTACACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttttattcttccataatgtattttttttgtttgtttgttttggtttcaaacagGGTGAAGCACAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCTGAAACTGCTGAGCTTGTTACACG
ataatgtatttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagaaaattaaaagcatacgtgttttttgagttattgtctactgttgtagttttattcttccataatgtattttttttgtttgtttgttttggtttcaaacagGGTGAAGCACAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCTGAAACTGCTGAGCTTGTTACACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT