Sequence
atgc intronic sequence ATGC exonic sequencegtgagtgccaaagaaaaattatgatcagttattacatatttcacactgtttcttttcttaaactctttaatgatctttaaaattatttgcttctgttatatttttgattgtggtcttgttctttgcagTTATCCTGGTTCCCCTTCTTTCTGTTCGATACAGATTGGATGGGAAGAGAAGTTTACCATGGGGATCCAACAGGAGATAGTTTGCATATGGAACTCTATG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G02860.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G02860.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os02g58080.1 (Oryza sativa), 3'ss of exon 9
gtgagtgccaaagaaaaattatgatcagttattacatatttcacactgtttcttttcttaaactctttaatgatctttaaaattatttgcttctgttatatttttgattgtggtcttgttctttgcagTTATCCTGGTTCCCCTTCTTTCTGTTCGATACAGATTGGATGGGAAGAGAAGTTTACCATGGGGATCCAACAGGAGATAGTTTGCATATGGAACTCTATG
| ||| | || | || | || | || ||| || | | | ||| ||| || | || | | || ||| |||| || | |||||||||| || ||||| ||||| || || || ||||| || ||||||||| | || |||||||||||||| |||| || | | | | || ||||
--gtatgctaccttaagacatctatgcatgtatatcagctgcatgctgattgtctctt---actgttttggaatttgtagattgatggtgttcatccatatcgtt-------------tgctttgcagTTGTCGTGGTTTCCCTTTTTCCTTTTTGATACTGACTGGATGGGACGTGAGGTTTACCATGGGGACCCAAATGGCAACTTGAGTGAAAGGAAAGCTTATG
upper sequence: AT2G02860.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G145107_T03 (Zea mays), 3'ss of exon 9
gtgagtgccaaagaaaaattatgatcagttattacatatttcacactgtttcttttcttaaactctttaatgatctttaaaattatttgcttctgttatatttttgattgtggtcttgttctttgcagTTATCCTGGTTCCCCTTCTTTCTGTTCGATACAGATTGGATGGGAAGAGAAGTTTACCATGGGGATCCAACAGGAGATAGTTTGCATATGGAACTCTATG
| | || || ||| || | | | | |||| || |||| || ||||| | || | |||| |||| | || | | |||||||| || ||||| ||||| || || || || || || ||||||||| | |||||||||||||||||||||| |||||| | | | || ||||
-----------------------gtacgctac--cagattacata-tatacatgcctaccgactccttgctgatggtttgttttattcgaggttgatg-atttacccttgttttattttgccttgcagTTGTCATGGTTTCCCTTTTTCCTTTTTGACACTGACTGGATGGGACGCGAAGTTTACCATGGGGATCCAAATGGAGATTTGAGTGAGAGGAAAGCTTATG
upper sequence: AT2G02860.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA18G15950.1 (Glycine max), 3'ss of exon 10
gtgagtgccaaagaaaaattatga-----tcagttattacatat---ttcacactgtttcttttcttaaactctttaa--tgatctttaaaatt---atttgcttctgttatatttttgattgtggtcttgttc-tttgcagTTATCCTGGTTCCCCTTCTTTCTGTTCGATACAGATTGGATGGGAAGAGAAGTTTACCATGGGGATCCAACAGGAGATAGTTTGCATATGGAACTCTATG
|| || | | | || | || ||| || | | |||| | || | || | || ||| | | || || ||||| || | | || ||| || ||| ||||||| || ||||| |||||||||||||| ||||| ||||||||||| ||||||||||| ||||| ||||||| ||| | | || | | || || ||||
gtatgtactagtatttatttgcaaaggtttctgttgatatttgtgttttcaagtcggttgtgttgtgaatgctattagcctagtgttggtgcttcccatttgaaatccttcttatgttcatttcaatcctgtctacctgcagTTGTCATGGTTTCCCTTCTTTCTGTTTGATACGGATTGGATGGGCAGAGAAGTTTATCATGGTGATCCAAAAGGGGGCACTTCTGAAGTAGATCTTTATG
upper sequence: AT2G02860.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G40980.1 (Glycine max), 3'ss of exon 9
gtgagtgccaaagaaaaattatga-----tcagttattacatat---ttcacactgtttcttttcttaaactctttaatgatctttaaaattatttgcttctgttatatttttgat------tgtggtcttgttc-tttgcagTTATCCTGGTTCCCCTTCTTTCTGTTCGATACAGATTGGATGGGAAGAGAAGTTTACCATGGGGATCCAACAGGAGATAGTTTGCATATGGAACTCTATG
|| || | | | || | || | || || | | |||| | | || | || | || ||| | | | || ||| || || || | || | | || | | ||||||| || ||||| |||||||||||||| ||||| ||||||||||| ||||||||||| ||||| ||||||| ||| || | || | | || || ||||
gtatgtactagtatttatttgcaaaggtttctgctaatatttgtgttttcaaatcggttgtgttgtgaatgctattagcc-tagtgctggtgcttcccttttgaaatccttcttatgttccctttaatcctatctacctgcagTTGTCTTGGTTTCCCTTCTTTCTGTTTGATACGGATTGGATGGGGAGAGAAGTTTATCATGGTGATCCAAAAGGGGACACTTCTGAAGTAGATCTTTATG
upper sequence: AT2G02860.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv01s0026g01960.t01 (Vitis vinifera), 3'ss of exon 9
gtgagtgccaaagaaaaattatg--atcagtt--attac--atatttca---cactgtttcttttc---ttaaactctttaatgatctttaaaattatttgcttctgttatatttttg----attgtggtcttgttctt-----------------tgcagTTATCCTGGTTCCCCTTCTTTCTGTTCGATACAGATTGGATGGGAAGAGAAGTTTACCATGGGGATCCAACAGGAGAT-AGTTTGCATATGGAACTCTATG
|| |||||| || | ||| | || || || | ||| | || || | | ||| ||| | |||| |||| || | | || |||||| || ||| ||| |||||| | ||| ||||| | |||||||| ||||||||||| || ||||| ||||||||||| ||||||||||| ||||||||||| | ||| ||| ||| |||| | || ||||
gtaagtgcctcagtagttacatgtcaccaattttgtttccaatactgcatggcaatatcaaatttgaaattagcttgtttattgattattgatcattagtgtttctgtgtaatggttgctctgttgaggtcttttccttgatattatactcctgtatgcagCTGTCCTGGTTTCCCTTCTTTCTTTTTGATACGGATTGGATGGGTAGAGAAGTTTATCATGGGGATCCTAAAGGGGATGAGTCTGCA-GTTAAAGCATATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttaaaattatttgcttctgttatatttttgattgtggtcttgttctttgcagTTATCCTGGTTCCCCTTCTTTCTGTTCGATACAGATTGGATGGGAAGAGAAGTTTACCATGGGGATCCAACAGGAGATAGTTTGCATATGGAACTCTATG
ttttgat putative branch site (score: 4)
tcttgttcttt putative PPT
aaaattatttgcttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtgccaaagaaaaattatgatcagttattacatatttcacactgtttcttttcttaaactctttaatgatctttaaaattatttgcttctgttatatttttgattgtggtcttgttctttgcagTTATCCTGGTTCCCCTTCTTTCTGTTCGATACAGATTGGATGGGAAGAGAAGTTTACCATGGGGATCCAACAGGAGATAGTTTGCATATGGAACTCTATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT