Sequence
atgc intronic sequence ATGC exonic sequence...tttgcattaatctcctttggaagtttcctattttagttatttatatgacctttccatataatcggagcgtaataagatggctctttcgtgtatcgatcagGCTTTTTCTACAGTAGGAACTCCCGATTACATTGCCCCTGAGGTGCTGCTGAAGAAAGGGTATGGAATGGAGTGTGATTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G30640.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G30640.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os05g43570.1 (Oryza sativa), 3'ss of exon 6
tttgcattaatctcctttggaagtttcctattttagttatttata-tgacctttccatataatcgga-gcgtaataagatggctctttcgtgtatcgatcagGCTTTTTCTACAGTAGGAACTCCCGATTACATTGCCCCTGAGGTGCTGCTGAAGAAAGGGTATGGAATGGAGTGTGATTG
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gccacgttgg-caagtgaatatgtacatgagtctagttttctaggctctcatcaatatatggtagtatgcttagttatact-cttttttttttggcatgcagGCATATTCAACGGTTGGTACTCCTGATTACATTGCTCCAGAGGTTCTGCTGAAGAAAGGATATGGAATGGAATGTGACTG
upper sequence: AT1G30640.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os12g19290.1 (Oryza sativa), 3'ss of exon 5
tttgcattaatctcctttggaagtttcctattttagttatttatatgacctttccatataatcggagcgtaataagatggctctttcgtgtatcgat--cagGCTTTTTCTACAGTAGGAACTCCCGATTACATTGCCCCTGAGGTGCTGCTGAAGAAAGGGTATGGAATGGAGTGTGATTG
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-gtcgatagaaaattgtagaaaaaatggcatggtaatcatttgtttg-ccaaagagccttggcagtgtgttttttatgtatttactttcatgataattgcagGCTTATTCAACAGTTGGTACACCTGATTACATTGCTCCGGAGGTACTATTGAAGAAAGGATATGGAATGGAGTGTGACTT
upper sequence: AT1G30640.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G049088_T02 (Zea mays), 3'ss of exon 5
--tttgcattaatctcctttggaagtttcctattttagttatttatatgacctttccatataatcggagcgtaataagatggctctttcgtgtatcgatcagGCTTTTTCTACAGTAGGAACTCCCGATTACATTGCCCCTGAGGTGCTGCTGAAGAAAGGGTATGGAATGGAGTGTGATTG
| || | | |||| | | | | | | || | | || ||||| | | | || | || | ||| || | |||||| ||||| || || || || ||||||||||| || ||||| || ||||||||||| ||||||||||| ||||| ||
catatggaatggctcagattggtcatctgtt-taaaactcatgcctggttctgtttcatatccttgactc-tattggtgtgcatggttcatgaaatttatagGCTTACTCTACTGTTGGTACACCTGATTACATTGCACCCGAGGTACTCCTGAAGAAAGGATATGGAATGGAATGTGACTG
upper sequence: AT1G30640.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G375904_T01 (Zea mays), 3'ss of exon 5
------tttgcattaatctccttt--ggaagtttcctattttagttatttatatgacctttccatataatcggagcgtaataagatggctctttcgtgtatcgatcagGCTTTTTCTACAGTAGGAACTCCCGATTACATTGCCCCTGAGGTGCTGCTGAAGAAAGGGTATGGAATGGAGTGTGATTG
| ||| | | ||| ||| ||||| || | | | || || | | | | || | | | ||| | | ||||| | || ||||| || || || ||||| ||||| || || ||||| ||||||||||| ||||||| ||||||||| ||
tgtctatcaagattccccccttttccataagcttccttcttgctgcgctgaggt-acacttgagcacagttgacatgt--ttaatcgcaattttgggaca-----cagGCATACTCAACAGTCGGTACACCTGATTATATTGCTCCAGAAGTGCTACTGAAGAAAGGATATGGAACGGAGTGTGACTG
upper sequence: AT1G30640.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 6
tttgcattaatctcctttggaagtttcctattttagttatttatatgacctttccatataatcggagcgtaataag-----atggctctttcgtgtatcgatcagGCTTTTTCTACAGTAGGAACTCCCGATTACATTGCCCCTGAGGTGCTGCTGAAGAAAGGGTATGGAATGGAGTGTGATTG
| ||| | | | | ||||| | | | || ||||| | ||| | | | || | ||| || | | |||||| ||| ||||| || |||||||| ||||||||||| || || |||||||||||||| ||||||||||||||||||||
-----gccactctggactacacttcttttatttgaataaaaatctcaggtattggatatattttgagtctgttttgtatttatagttctgtcatatgctatctagGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG
upper sequence: AT1G30640.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------------------------tttg-cattaatctcctttggaagtttcctatttt-agttatttatatgacctttccat-ataatcggagcgtaataagatggctctttcgtgtatcgatcagGCTTTTTCTACAGTAGGAACTCCCGATTACATTGCCCCTGAGGTGCTGCTGAAGAAAGGGTATGGAATGGAGTGTGATTG
|||| ||| || || | | || || || || | | || | | | | || ||| | | || | || | | |||||| | ||| ||||| || ||||| ||||| ||||| ||||| || |||||||||||||| ||||| ||||||||||| ||
gtaatcttctttgcattccattttgcagtagctcttcgtcctcttcacaatttctgcctttgtcatagatgtcatcttctaggtttgcatacagaggagtgcaagtggcactccattgatcatctgtaatctcaagtattgacacaaagtttcgcattcagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgacctttccatataatcggagcgtaataagatggctctttcgtgtatcgatcagGCTTTTTCTACAGTAGGAACTCCCGATTACATTGCCCCTGAGGTGCTGCTGAAGAAAGGGTATGGAATGGAGTGTGATTG
taataagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgcattaatctcctttggaagtttcctattttagttatttatatgacctttccatataatcggagcgtaataagatggctctttcgtgtatcgatcagGCTTTTTCTACAGTAGGAACTCCCGATTACATTGCCCCTGAGGTGCTGCTGAAGAAAGGGTATGGAATGGAGTGTGATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - -atctcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataaga