Sequence
atgc intronic sequence ATGC exonic sequencegtacttagccttgaaaccattctctgtactttattggttgacttttcactttccggaatcctgatgatgatcttattgcagGAGAAGCTATAGCTTTAGGTTTCGAGCATTACATTCTGGCTTTAGGAACTGCAGTGATGATACCTTCAATTCTTGTTCCTATGATGGGTGGAGATGAT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G34190.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G34190.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G12360.1 (Glycine max), 3'ss of exon 1
------------------------gtacttagccttgaaac--cattctctgtactttattggttgacttttcactttcc---------ggaatcctgatgatgatcttattgcagGAGAAGCTATAGCTTTAGGTTTCGAGCATTACATTCTGGCTTTAGGAACTGCAGTGATGATACCTTCAATTCTTGTTCCTATGATGGGTGGAGATGAT
| | | |||| |||| | ||| |||| || | | || | ||| | | || | | | | || | ||| || | |||||||| |||||| ||||||||||| |||| || ||||||||||||||||| |||||| |||| || ||| ||||||||||| ||||
gtatgcaactgtgcattacaagcttcaatcttttctcaaactgcattgtttgtgctttgtttcctaggtatttatttttcactgtgagtgatatatatacgttaaactgttaacagCTGAGACAATAGCTTTGGGTTTCCAGCATTACATTTTGGCCTTGGGAACTGCAGTGATGATCCCTTCATTTCTGGTGCCTGTGATGGGTGGAAGTGAT
upper sequence: AT2G34190.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA04G06750.1 (Glycine max), 3'ss of exon 1
----------------------gtacttagcct--tgaaaccatt------ctctgtactttattggttgacttttcactttccggaatcctgatgatgatcttattgcagGAGAAGCTATAGCTTTAGGTTTCGAGCATTACATTCTGGCTTTAGGAACTGCAGTGATGATACCTTCAATTCTTGTTCCTATGATGGGTGGAGATGAT
| | ||| | ||||| ||| | ||| | | ||| || ||| ||| | || | ||| || | ||| || | |||| | | |||||| ||||||||||| |||| |||||||||||||| ||||| |||||| ||||||| ||| ||||||||||| ||||
gtatgcccacttcctcaactgcattttcagcttcatgaaaagattgaacttttttgtgtgtatgttgttcacattttggttttaatgagaatgttt-tgaactgttaacagTGGAGACAATAGTTCTTGGTTTCCAGCATTACATTTTGGCCTTAGGAACTGCAGTCATGATTCCTTCATTTCTTGTGCCTTTGATGGGTGGAAGTGAT
upper sequence: AT2G34190.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G06840.1 (Glycine max), 3'ss of exon 1
--------------------gtacttagccttgaaaccattctctgtactttattggttgacttttcactttccggaatcctgatgatgatcttattgcagGAGAAGCTATAGCTTTAGGTTTCGAGCATTACATTCTGGCTTTAGGAACTGCAGTGATGATACCTTCAATTCTTGTTCCTATGATGGGTGGAGATGAT
| | || | | | || ||||| ||| |||| ||| || | | ||| | | | | ||| || | |||| | | |||||| ||||||||||| |||| |||||||||||||| ||||| |||||| ||||||| ||| ||||||||||| ||||
gtatgctcacttcctcaactgcattttcagcttcattaaaagattgaacttttttgtgcacattttggttttaatgagtgtttttga--accgtttaacagTGGAGACAATAGTTCTTGGTTTCCAGCATTACATTTTGGCCTTAGGAACTGCAGTCATGATTCCTTCATTTCTTGTGCCTTTGATGGGTGGAAGTGAT
upper sequence: AT2G34190.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv10s0003g01460.t01 (Vitis vinifera), 3'ss of exon 1
--------gtacttagccttgaaaccattctctgtactttattggttgactt-ttcactttccgga----atcctgatgat--gatcttattgcagGAGAAGCTATAGCTTTAGGTTTCGAGCATTACATTCTGGCTTTAGGAACTGCAGTGATGATACCTTCAATTCTTGTTCCTATGATGGGTGGAGATGAT
| ||| ||| || ||| | || | | | ||| | ||| ||| | | ||| | ||| | | ||| || ||||||||| | || ||| | || ||||| |||| || || |||||||||||||| || ||| | ||||||||| ||||||||||| ||||
gtacgctctttcttgatcttttcttcaatcttgattctccaattgatgattggctcattttttgaatggtatctcactttctggatgtaaaaacagCGGAGGCTATAGCTCTGGGGTTCCAACACTACATCTTGGCCTTGGGGACTGCAGTGATGATTCCCTCATTCCTTGTTCCTCTGATGGGTGGAACTGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactttattggttgacttttcactttccggaatcctgatgatgatcttattgcagGAGAAGCTATAGCTTTAGGTTTCGAGCATTACATTCTGGCTTTAGGAACTGCAGTGATGATACCTTCAATTCTTGTTCCTATGATGGGTGGAGATGAT
tcctgat putative branch site (score: 3)
tcttatt putative PPT
atcttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttagccttgaaaccattctctgtactttattggttgacttttcactttccggaatcctgatgatgatcttattgcagGAGAAGCTATAGCTTTAGGTTTCGAGCATTACATTCTGGCTTTAGGAACTGCAGTGATGATACCTTCAATTCTTGTTCCTATGATGGGTGGAGATGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG