Sequence
atgc intronic sequence ATGC exonic sequencegtaaactttacaatgagtctcagatttgaaacaatttggccctaaatgattttagtgcataactgtttacattttatcgtcagGTGGTCTCAAATAGCTACTCGGCTTCCAGGTAGAACAGACAACGAGATCAAAAACTTTTGGAACTCGACATTGAAGAAGCGGCTTAAGAACAACAGCAAC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G08500.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G08500.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G052606_T01 (Zea mays), 3'ss of exon 1
--------gtaaactttacaatgagtctcagat---------ttgaaacaat--ttggccctaaatgattttagtgcataactgtttacattttatcgtcagGTGGTCTCAAATAGCTACTCGGCTTCCAGGTAGAACAGACAACGAGATCAAAAACTTTTGGAACTCGACATTGAAGAAGCGGCTTAAGAACAAC--AGCAAC
||| | | ||| | |||| || || | | || || || ||| | | | | || ||||| ||| |||||||||||| || ||| | ||| | || || | || |||||||||||||| ||||| |||||||| || | ||||||||||| ||||||| | |||
gtacgtacgtacgcatgacactttctctctgacagaaagatcctggatcgatcgtttgcttactgtgaaatcaaccctcacttgcg-acattatatt-ccagGTGGTCTCAGATTGCTGCCCGGTTGCCGGGGCGCACCGACAACGAGATCAAGAACTTCTGGAACTCCACCATCAAGAAGCGGCTCAAGAACAGCTCGGCA--
upper sequence: AT3G08500.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ38262 (Selaginella moellendorffii), 3'ss of exon 2
gtaaactttacaatgagtctcagatttgaaacaatttggccctaaatgattttagtgcataactgtttacattttatcgt-cagGTGGTCTCAAATAGCTACTCGGCTTCCAGGTAGAACAGACAACGAGATCAAAAACTTTTGGAACTCGACATTGAAGAAGCGGCTTAAGAACAACAGCAAC
|| | | ||| || ||| | |||||| || | | || || || | | | || | | ||||||| | ||||| || || | ||| || ||| |||||||||||||||| |||||||||||||||||| || |||| ||| | | | |
gtgtgtgctcgagcgag-ctggaattcg-----atttggtgtggaaatgtagcattggattgatgctgaattgtttccatacagGTGGGCGCAAATTGCGACGCAGCTCCCGGGTCGAACAGACAACGAGATTAAAAACTTTTGGAACTCGTGCCTGCGGAAGAAGCTACGTCAAGTTGGTATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaacaatttggccctaaatgattttagtgcataactgtttacattttatcgtcagGTGGTCTCAAATAGCTACTCGGCTTCCAGGTAGAACAGACAACGAGATCAAAAACTTTTGGAACTCGACATTGAAGAAGCGGCTTAAGAACAACAGCAAC
gcataac putative branch site (score: 3)
ttttatc putative PPT
taaatgattttagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaactttacaatgagtctcagatttgaaacaatttggccctaaatgattttagtgcataactgtttacattttatcgtcagGTGGTCTCAAATAGCTACTCGGCTTCCAGGTAGAACAGACAACGAGATCAAAAACTTTTGGAACTCGACATTGAAGAAGCGGCTTAAGAACAACAGCAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC