Sequence
atgc intronic sequence ATGC exonic sequence...ttgatataacatgagaaactcatataactgtatgttatcaaatgattaatagtttcccccacccccacctcttgattaatagctgtcatcatttttgtagGTAAAGAACTTCATCCTTATTGGCGATATCCATAAAAGCATATACTTTCTTAGTTGGAAAGAGCAGGGTGCTCAATTGAGCTTATTAGCCAAGGATTTTG
Basic information
species | Glycine max |
transcript | GLYMA09G28030.1 |
intron # | 23 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G28030.1 (Glycine max), 3'ss of exon 23
lower sequence: LOC_Os04g18010.1 (Oryza sativa), 3'ss of exon 23
ttgatataacatgagaaactcatataactgtatgttatcaaatg-attaatagtttcccccacccccacctcttgattaatagctgtcatcatttttgta---gGTAAAGAACTTCATCCTTATTGGCGATATCCATAAAAGCATATACTTTCTTAGTTGGAAAGAGCAGGGTGCTCAATTGAGCTTATTAGCCAAGGATTTTG
| |||||| || | | | || || | || | | | || ||| || | ||| || ||| |||| ||| || |||||| | | |||| ||||| ||||||||||| || ||||| || ||||||||||| ||| |||||||||| | | || || |||||||
gcatttcaacatgcataagc----tggcaatttgcaataatgtgcactgctttctttaatggttgtggtgtctgaataatcctctgagattgtttctgtaacagGTCAAAAACTTCGTTTTGTTTGGTGATATTCATAAAAGCATTTATTTTCTGAGCTGGAAAGAGCAAGGTTCTCAATTGAGTCTCCTGGCAAAAGATTTTG
upper sequence: GLYMA09G28030.1 (Glycine max), 3'ss of exon 23
lower sequence: AT5G51660.1 (Arabidopsis thaliana), 3'ss of exon 23
---------------------------------------ttgatataacatgagaaactcatataactg-tatgttatcaaatgattaatagtttcccccacccccacctcttgattaatagctgtcatcatttttgtagGTAAAGAACTTCATCCTTATTGGCGATATCCATAAAAGCATATACTTTCTTAGTTGGAAAGAGCAGGGTGCTCAATTGAGCTTATTAGCCAAGGATTTTG
||| | | | | || | | ||||| ||| | | ||||| | | | ||| | || || | | ||| |||| |||| ||||||||| |||| ||| | || |||||||||||||||||||| ||||| || || || | ||| | |||||| ||||||| |||||||
gtacgttttacttccttggccagattgcctagtgctgtgttggttttatgagctaactttactaaactgacctgtcttggctctgaggacagttttcttttacgtga--tctggctttgtaaattcttctttacttgcagGTTAAGAGTTTCATCCTTCTTGGTGATGTTCACAAAAGCATATACTTTCTTAGCTGGAAGGAACAAGGGTCCCAACTTAGCTTACTAGCCAAAGATTTTG
upper sequence: GLYMA09G28030.1 (Glycine max), 3'ss of exon 23
lower sequence: Vv16s0022g01860.t01 (Vitis vinifera), 3'ss of exon 23
-ttgatataacatgagaaactcatataactgtatgttatcaaatgattaatagtttcccccacccccacct--cttgattaatagctgtcatcatttttgtagGTAAAGAACTTCATCCTTATTGGCGATATCCATAAAAGCATATACTTTCTTAGTTGGAAAGAGCAGGGTGCTCAATTGAGCTTATTAGCCAAGGATTTTG
| | || | ||| | || | ||| | | |||| | | | | |||||| || | | ||| ||| |||| ||||| || ||||| | || || || || | |||||| ||||||||||||||||| || ||||| |||||| | | ||||||||| || |||||||
accagtgcattgtggttcatgcatgttgttgca--acatctgctccatgttagtgccattttttcatgtttgatcttattaatttct-taaacatcgttgcagGTTAAGAATTTTATCCTCCTAGGTGACATTCACAGAAGCATTTACTTTCTTAGTTGGAAGGAACAGGGAGCTCAACTTAACTTATTAGCGAAAGATTTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaatagtttcccccacccccacctcttgattaatagctgtcatcatttttgtagGTAAAGAACTTCATCCTTATTGGCGATATCCATAAAAGCATATACTTTCTTAGTTGGAAAGAGCAGGGTGCTCAATTGAGCTTATTAGCCAAGGATTTTG
gattaat putative branch site (score: 3)
tcattttt putative PPT
ttgattaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgatataacatgagaaactcatataactgtatgttatcaaatgattaatagtttcccccacccccacctcttgattaatagctgtcatcatttttgtagGTAAAGAACTTCATCCTTATTGGCGATATCCATAAAAGCATATACTTTCTTAGTTGGAAAGAGCAGGGTGCTCAATTGAGCTTATTAGCCAAGGATTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - acatgag
- - - - - - - - - - - - - - tgtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgtca