Sequence
atgc intronic sequence ATGC exonic sequence...ccaaaaaaatgacattttcatttgccaaaaacatacatatagatgatgtgtagcctcttaattaccttcatttttacgtttaaattttctccgattgcagTGGTTTTCATTGGATCTACCCTTTTTGCTTTACAACAGTTGTCTGGGATAAATGCTGTGTTCTATTTCTCATCAACTGTCTTCAAGAAAGCTGGTGTACC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G79820.4 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G79820.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os02g17500.1 (Oryza sativa), 3'ss of exon 9
--ccaaa--aaaatgacattttcatt-tgccaaaaacatacatatagatgatgtgtagcctcttaattaccttca--tttttacgtt-taaattttctccgattgcagTGGTTTTCATTGGATCTACCCTTTTTGCTTTACAACAGTTGTCTGGGATAAATGCTGTGTTCTATTTCTCATCAACTGTCTTCAAGAAAGCTGGTGTACC
||| ||| ||| |||| || | | | | | | | | | |||| | ||| | | || || | | | |||| ||||| ||||| | || || ||||||||||||||||| || || |||||| ||||||||||||||||||||||||| |||| | | ||||| ||
gtacaagctgttatgtgttttccattctgttgtgtatttgcgctaaactataaccttatttatgtttggccttgaagtttgttcattacaagtccctttttgctacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAAATTCTGTGTTCTATTTCTCATCAACTGTGTTCAGAAGTGTGGGTGTGCC
upper sequence: AT1G79820.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G412899_T05 (Zea mays), 3'ss of exon 9
------ccaaaaaaatgacattttcatt-tgccaaaaacatacatatagatgatgtgtagcctcttaattaccttcattt-ttacgtttaaattttctccgattgcagTGGTTTTCATTGGATCTACCCTTTTTGCTTTACAACAGTTGTCTGGGATAAATGCTGTGTTCTATTTCTCATCAACTGTCTTCAAGAAAGCTGGTGTACC
| || | |||| || || | | | ||| || || || | | | || || |||| | | | | | |||| ||||| ||||| | || || ||||||||||||||||| || || |||||| ||||||||||||||||||||||||| |||| | | || || ||
gtacaagctgttctatatcctttttgttgtgtttatggacttctaataacctgagttcagtctgtctgtgaagtttgttcattaca---agttccttttttggtacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAAATTCTGTGTTCTATTTCTCATCAACTGTATTCAGAAGTGTGGGGGTGCC
upper sequence: AT1G79820.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G21860.1 (Glycine max), 3'ss of exon 9
------------------------------------------------------------ccaaaaaaatgacattttcatttgccaaaaacatacatata-gatgatgtgtagcc-tcttaattaccttcatttttacgtttaaattttctccgattgcagTGGTTTTCATTGGATCTACCCTTTTTGCTTTACAACAGTTGTCTGGGATAAATGCTGTGTTCTATTTCTCATCAACTGTCTTCAAGAAAGCTGGTGTACC
||| | || | |||| | | | | | || | | ||| ||||| ||| | | | | |||| | |||||||| | |||||||||||||| |||||||| || || ||| | ||||| ||||||||||| ||||||||||| ||||||||||| | | |||||||||
gtacataactacatatcataatattttattcttttggaacagtagtgtatcttttagacgattgcttaatcatatcataatttctaattcatttgtttttgcaatagtatatagttgtcttatttatggttgctaaatcact-aaatgcatt----ttgcagTGATGTTCATTGGATCTACACTTTTTGCGTTGCAGCAGCTATCTGGCATAAATGCTGTTTTCTATTTCTCTTCAACTGTCTTTGAAAGTTTTGGTGTACC
upper sequence: AT1G79820.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G02200.1 (Glycine max), 3'ss of exon 9
------------------------------------------------------------ccaaaaaaatgacattttcatttgccaaaaacatacatatagatga---tgtgtagcctcttaattaccttcatttttacgtt--taaattttctccgattgcagTGGTTTTCATTGGATCTACCCTTTTTGCTTTACAACAGTTGTCTGGGATAAATGCTGTGTTCTATTTCTCATCAACTGTCTTCAAGAAAGCTGGTGTACC
|| | || | |||| | |||| ||| | | | | | | ||| | | || | || || | ||||| | |||||||| | |||||||||||||| |||||||| | || ||| | ||||| ||||||||||| ||||||||||| ||||||||||| | | |||||||||
gtacataactacatatcataatattttatttttttggaacagtagtgtatcttttagatgattgctcgatcatatcataattt-ctaaaatcatttgtttttgtaagagtatatagttgcgtcttttttatggttgctaaatcactaaatgcatt----ttgcagTGATGTTCATTGGATCTACACTTTTTGCGCTGCAGCAGCTATCTGGCATAAATGCTGTTTTCTATTTCTCTTCAACTGTCTTTGAAAGTTTTGGTGTACC
upper sequence: AT1G79820.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv09s0002g04380.t01 (Vitis vinifera), 3'ss of exon 8
ccaaaaaaatgacattttcatttgccaaaaacatacatatagatgatgtgtagcctcttaattaccttcatttttac---gtttaaattttctccgattgcagTGGTTTTCATTGGATCTACCCTTTTTGCTTTACAACAGTTGTCTGGGATAAATGCTGTGTTCTATTTCTCATCAACTGTCTTCAAGAAAGCTGGTGTACC
|| || | || || || || | | | || || ||||| | |||| | | | ||||||||||||||||||| | ||| ||||||||||||||| | ||||| ||||||||||||||||||||||| |||||||||||||| |||||| |||||
---------------------------gtaatatgc---taaattattagtgttttatccactatgtttattttgagttgatttatctgaatttatttcacagTGGTTTTCATTGGATCAAGCCTATTTGCTTTACAACAGCTTTCTGGCATAAATGCTGTGTTCTATTTCTCTTCAACTGTCTTCAAAGGAGCTGGAGTACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtgtagcctcttaattaccttcatttttacgtttaaattttctccgattgcagTGGTTTTCATTGGATCTACCCTTTTTGCTTTACAACAGTTGTCTGGGATAAATGCTGTGTTCTATTTCTCATCAACTGTCTTCAAGAAAGCTGGTGTACC
tcttaat putative branch site (score: 3)
ttttctcc putative PPT
ttcatttttacgttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccaaaaaaatgacattttcatttgccaaaaacatacatatagatgatgtgtagcctcttaattaccttcatttttacgtttaaattttctccgattgcagTGGTTTTCATTGGATCTACCCTTTTTGCTTTACAACAGTTGTCTGGGATAAATGCTGTGTTCTATTTCTCATCAACTGTCTTCAAGAAAGCTGGTGTACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG