Sequence
atgc intronic sequence ATGC exonic sequencegtactaaccaaaccgtctttcttcttacagaatgtttgttttgtgtgataaaccaaactggcttttttctttcttacagAGCACTGAGCAACAAGTACAAGGTGTCTTGAACCTGATTGATCTTGCGGGGAGTGAGCGTTTATCGAAGAGTGGATCAACCGGAGATAGACTTAAAGAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G54670.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G54670.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA12G16580.1 (Glycine max), 3'ss of exon 14
----------------------------------------------gtactaaccaa--accgtcttt-cttcttacagaatgtttgttttgtgtgataaaccaaactggcttttttctttcttacagAGCACTGAGCAACAAGTACAAGGTGTCTTGAACCTGATTGATCTTGCGGGGAGTGAGCGTTTATCGAAGAGTGGATCAACCGGAGATAGACTTAAAGAAA
|| | ||| || ||| | | ||| | || ||| | | || ||| || |||| |||||||| ||||||||||| ||||||||||||||||| ||||||| |||||||| || || || ||||| | || ||||||||||||||||| || | | |||||||
gtaaagatgtttctcttttgacaataactaaaaccatgtcctatgtttagttttcaatttccatctcaaccttcaacaaacacactgacttgcatcacaatgcaaccta--ttttatctttcttccagAGCACTGACCAACAAGTACAAGGTGTTCTGAACCTCATTGATCTAGCTGGTAGCGAGCGGCTTTCAAAGAGTGGATCAACCGGGGACCGGTTGAAAGAAA
upper sequence: AT5G54670.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA06G41600.1 (Glycine max), 3'ss of exon 13
------------------------------------gtacta-accaaaccgt---ctttcttcttacagaatgtt--------tgttttgtgtgataaaccaaactggcttttttctttcttacagAGCACTGAGCAACAAGTACAAGGTGTCTTGAACCTGATTGATCTTGCGGGGAGTGAGCGTTTATCGAAGAGTGGATCAACCGGAGATAGACTTAAAGAAA
|| ||| | || | || | ||| | | || | || ||| || | || ||| || ||| |||||||| ||||||||||| ||||||||||||||||| ||||||| ||||||||||| || || ||||| | || |||||||||||||| || || | | |||||||
gtaaagattttctattatgacaatgactaaaaccatgttctatattcaatttttaatttccatctcaaccagtgatagacacactgacttgcgtcacaatgcaaccta---tttgtctttcttccagAGCACTGACCAACAAGTACAAGGTGTTCTGAACCTTATTGATCTTGCTGGTAGCGAGCGGCTTTCAAAGAGTGGATCAACTGGGGACCGGTTGAAAGAAA
upper sequence: AT5G54670.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA13G36230.2 (Glycine max), 3'ss of exon 14
-------------------gtactaaccaaaccgtctttcttcttacagaatgtttgttttgtgtgataaaccaaactg-gcttttttctttcttacagAGCACTGAGCAACAAGTACAAGGTGTCTTGAACCTGATTGATCTTGCGGGGAGTGAGCGTTTATCGAAGAGTGGATCAACCGGAGATAGACTTAAAGAAA
| ||| |||| | |||| | || || | | | | |||| || | | |||| |||||||||| ||||||||||||||| | | || || ||||||||||| |||||||| ||| | || | ||||||||||||||| || || | ||||| |
gtatggttgttctcctttgacaataattgaaccatgtttcatac-actcgataacaatctaacaagc--attcaaattgcaacctgattgttctactagAGCACTGACCAACAAGTACAAGGTATTCTAAATCTCATTGATCTTGCTGGGAGTGAACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGA
upper sequence: AT5G54670.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA12G34330.1 (Glycine max), 3'ss of exon 13
--------------------gtactaaccaaaccgtctttcttcttacagaatgtttgttttgtgtgataaaccaaactg--gcttttttctttcttacagAGCACTGAGCAACAAGTACAAGGTGTCTTGAACCTGATTGATCTTGCGGGGAGTGAGCGTTTATCGAAGAGTGGATCAACCGGAGATAGACTTAAAGAAA
| ||| |||| | |||| | || ||| | | | | |||| || | | | |||| |||||||||| ||||||| ||||||| | | || || ||||||||||| |||||||||||| | || | ||| || ||||| || || || | |||||||
gtatggttgtttctcctctgacagtaattgaaccatgtttcatac-actcaatagcaatctaacaagc--attcaaattgcaaccaatcttgttctgctagAGCACTGACCAACAAGCACAAGGTATTCTAAATCTCATTGATCTTGCTGGGAGTGAGCGTCTTTCAAGGAGCGGGTCAACTGGGGACCGATTGAAAGAAA
upper sequence: AT5G54670.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv19s0014g05070.t01 (Vitis vinifera), 3'ss of exon 13
-------gtactaaccaaaccgtctttcttcttacag-aatgtttgtt-ttgtgtgataaaccaaactggcttttttctttc--tta-------cagAGCACTGAGCAACAAGTACAAGGTGTCTTGAACCTGATTGATCTTGCGGGGAGTGAGCGTTTATCGAAGAGTGGATCAACCGGAGATAGACTTAAAGAAA
|| | | || ||| | | |||| ||| | | || ||| ||| | | ||| | |||| ||| ||||||||||| ||||||||||||||||| |||||||| |||||||||||||| ||||| || | || |||||||||||||| || || | | |||||||
gtataaagtcttcatggtgccctctgtgctgatacattgatgctcttgattatgttttaactctgttttctctttgtttttcacttatattgaccagAGCACTGAACAACAAGTACAAGGTGTTTTGAACCTTATTGATCTTGCGGGCAGTGAACGACTTTCTAAGAGTGGATCAACAGGGGACCGTTTGAAAGAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttacagaatgtttgttttgtgtgataaaccaaactggcttttttctttcttacagAGCACTGAGCAACAAGTACAAGGTGTCTTGAACCTGATTGATCTTGCGGGGAGTGAGCGTTTATCGAAGAGTGGATCAACCGGAGATAGACTTAAAGAAA
ttcttac putative branch site (score: 2)
ctggcttttttctttc putative PPT
ttttttctttctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactaaccaaaccgtctttcttcttacagaatgtttgttttgtgtgataaaccaaactggcttttttctttcttacagAGCACTGAGCAACAAGTACAAGGTGTCTTGAACCTGATTGATCTTGCGGGGAGTGAGCGTTTATCGAAGAGTGGATCAACCGGAGATAGACTTAAAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA