Sequence
atgc intronic sequence ATGC exonic sequencegttcataaacaagcctatttgtttcttgttgatattgtgctacattttttttacattacatgactttcttattttggtgaacaaaagGCTCATATTCAGGAGCTTGAAGAGGAAGTGAAGCTACTCAAGAATCTCTCTCATCCAAATATAGTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G54960.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G54960.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os08g32600.1 (Oryza sativa), 3'ss of exon 2
------------gttcataaacaagcctatttgtttcttgttgat--attgtgctaca--------ttttttttacattacatgactttcttattttggtgaacaaa------------agGCTCATATTCAGGAGCTTGAAGAGGAAGTGAAGCTACTCAAGAATCTCTCTCATCCAAATATAGTT
| ||| || | ||| | | | || || ||||||| | || ||| || | | | | | || || | | ||| || || ||||||||| || |||||||||||||||||||| ||||| || || || || |||
gtgagtggctttgctcaattacttgtttatctttgttttcctggccaattgtgccattgaaatagtcttctttaacctcctctaagctctaagtgttcgtaattggatttttttttattagGGGCACATAAGGGAGCTTGAGGACGAAGTGAAGCTACTCAAGAACCTCTCACACCCCAACATTGTT
upper sequence: AT1G54960.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: AC197029.3_FGT003 (Zea mays), 3'ss of exon 2
-------------gttcataaacaagcctatttgtttcttgttgatattgtgctacattttt---tttacattacatgactttcttattttggtgaacaaaagGCTCATATTCAGGAGCTTGAAGAGGAAGTGAAGCTACTCAAGAATCTCTCTCATCCAAATATAGTT
|| ||||| || | || || || | ||| | ||| | ||| || | | | | ||| | |||||||||| | ||||| ||||| |||||||||||||||||||| || ||||| || || || |||
gtgagtagcattttttaataaaaaattgtgttctcggggaattagagccttgaggcttttgtgagtttgtctgacacgatgtgccttctgtggcta------gGCTCATATTAAAGAGCTCGAAGAAGAAGTGAAGCTACTCAAGAACCTGTCTCACCCCAACATTGTT
upper sequence: AT1G54960.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0128g00430.t01 (Vitis vinifera), 3'ss of exon 2
--------------gttcataaacaagcctatttgtttcttgttgat--attgtgctacattttttttacattacatgactttcttattttggtgaacaaaagGCTCATATTCAGGAGCTTGAAGAGGAAGTGAAGCTACTCAAGAATCTCTCTCATCCAAATATAGTT
|| | | | | |||| || | |||| || | | ||| | | || || ||| || || || | ||||||||||| ||| |||||||| ||||||||||| || |||||||||||||||||||| || |||
gagcaatgtgcaattttggttgatttggc-atttattgtgaggtgattaatcaaagaatagcatttattgactaagtgtcttgattgtt--aatgctaagtagGCTCATATTAGGGAACTTGAAGAAGAAGTGAAGCTTCTTAAGAATCTCTCTCATCCAAACATTGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattgtgctacattttttttacattacatgactttcttattttggtgaacaaaagGCTCATATTCAGGAGCTTGAAGAGGAAGTGAAGCTACTCAAGAATCTCTCTCATCCAAATATAGTT
tacattttttttacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcataaacaagcctatttgtttcttgttgatattgtgctacattttttttacattacatgactttcttattttggtgaacaaaagGCTCATATTCAGGAGCTTGAAGAGGAAGTGAAGCTACTCAAGAATCTCTCTCATCCAAATATAGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC