Sequence
atgc intronic sequence ATGC exonic sequence...tgaatggaacatcaaaatgtccatggaaattctcagcattgtgtatcaaccatgttcattcttttagttatatgtcattttgaatcatattactgtgcagGGATACTGCAGGACAGGAGAGATTTCGAAGTCTAATACCAAGTTATATCAGAGATTCTTCTGTTGCTGTAATTGTCTATGATGTTGCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G10260.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G10260.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G128771_T01 (Zea mays), 3'ss of exon 2
tgaatggaacatcaaaatgtccatggaaattctcagcattgtgtatcaaccatgttcattcttttagttatatgtcat--tttgaatcatattactgtgcagGGATACTGCAGGACAGGAGAGATTTCGAAGTCTAATACCAAGTTATATCAGAGATTCTTCTGTTGCTGTAATTGTCTATGATGTTGCAA
||| ||| | || | | ||||||| | || | | || | ||| | | | || |||| |||||||||||||||||||||||| ||| | ||||| || ||||| || ||||| || ||||||||||| || |||| |||||||| | |
nnnnnnnnnnnnnnnnnnncacattactatttgagttttggtagctttgtta-gttcattttcttggagaacagttagcatttcattgttcttgctgt-cagGGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA
upper sequence: AT5G10260.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G14390.1 (Glycine max), 3'ss of exon 2
-------------------------------------------------------tgaatggaacatcaaaatgtccatggaaattctcagcattg-tgtatcaaccatg--ttcattcttttagttatatgtcattttgaatcatatta-ctgtgcagGGATACTGCAGGACAGGAGAGATTTCGAAGTCTAATACCAAGTTATATCAGAGATTCTTCTGTTGCTGTAATTGTCTATGATGTTGCAA
| | |||| | | || | | | || || | | | | | | || || |||| || | | | || || ||| || ||||||||||||||| || || |||||| ||||||| || ||||| || || ||||||||||||||||| || || || ||||||||||| |
gtaggatgaattcctcttcaaatcatatatacaagctcagtctttttatatttgtttgtttatttttcaacaattatattagagtgcacattgctggtatgcctagtaggcattgtttatttttacaatttctgagcttagtatatgttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTATAGTATATGATGTTGCTA
upper sequence: AT5G10260.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G31200.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------tgaatggaacatcaaaatgtccatggaaattctcagcattg---tgtatcaaccatgttcattcttttagttatatgtcattttgaatcatatta-ctgtgcagGGATACTGCAGGACAGGAGAGATTTCGAAGTCTAATACCAAGTTATATCAGAGATTCTTCTGTTGCTGTAATTGTCTATGATGTTGCAA
|| | |||| | | || | | | || || | | | || || || | || | | | || || ||| || ||||||||||||||| || || |||||| ||||||| || ||||| || || ||||||||||||||||| || || || ||||||||||| |
gtaggatgactcctcttcaaatcataaatacaagctcagtctatttatatttgttttatttttcaacaattatattagagtacacattgctggtacgccttataggcactctttattcttacaatttctgagcttagtatatgttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCGGTTATAGTATATGATGTTGCTA
upper sequence: AT5G10260.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G38110.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------tgaatggaacatcaaaatgtccatggaaattctcagcattgtgtat-caaccatgttcattcttttagttatatgtcattt-tgaatcatatt---actgtgcagGGATACTGCAGGACAGGAGAGATTTCGAAGTCTAATACCAAGTTATATCAGAGATTCTTCTGTTGCTGTAATTGTCTATGATGTTGCAA
| | | | | |||| | || | ||| || || |||| ||| | || | || | || ||||| | || || |||| ||| ||||||||||||||| || || || ||| ||||||| || ||||| || || ||||||||||||||||| || ||||| |||||||| || |
gtaggccatattcctcttcaactcataccacaagatctatttatatttgtttttttgtattttaaaagttatattagatttcacattgttatgtaggcaattttttttaccgttct--ttgtatgttaaaagtgtgtcgtattttaacttcacagGGATACTGCAGGGCAAGAAAGGTTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTATTGTATATGATGTAGCCA
upper sequence: AT5G10260.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G02040.1 (Glycine max), 3'ss of exon 2
-------------------------------------------tgaatggaacatcaaaatgtccatggaaattctcagcattgtgtatcaaccatgttcattcttttagttatatgtcatt-ttgaatcatatt---actgtgcagGGATACTGCAGGACAGGAGAGATTTCGAAGTCTAATACCAAGTTATATCAGAGATTCTTCTGTTGCTGTAATTGTCTATGATGTTGCAA
| | |||| | || | ||| || ||||||| || | || | | || || ||||| | ||| ||||||| ||| ||||||||||||||| || || |||||| ||||||| || ||||| || || ||||||||||||||||| || |||| || ||||| || |
gtaggccatattcctctttaactcatgccacaagacctatttatatttttttttctaaaagttatattagatttcacattgttgtgtaggcactttttttaacccattctttgtatgttaaaattgtttcatattttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTGATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTGTTGTATACGATGTAGCCA
upper sequence: AT5G10260.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 2
tgaatggaacatcaaaatgtccatgg--aaattctcagcat-tgtgtatcaaccatgttcattcttttagttatatgtcattttgaatcatattactgtgcagGGATACTGCAGGACAGGAGAGATTTCGAAGTCTAATACCAAGTTATATCAGAGATTCTTCTGTTGCTGTAATTGTCTATGATGTTGCAA
|| ||| ||||| ||| | | | || || || ||||| | | | || ||| ||||| | | |||||| | | | | |||||||||||| || || || |||||| | ||||| |||||||| || || ||||||||||| |||||||| ||||| |||||||||| ||
-gattggtttctcaaattgtttaggtttacatgctgtagatacttgtattatttgtttatatacttctagtt-tctaaaattttggcttttgaaatt-cacagGGATACTGCTGGCCAAGAAAGATTTAGGAGTCTTATACCAAGCTACATAAGAGATTCTTCAGTTGCTGTGATTGTTTATGATGTTGGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaaccatgttcattcttttagttatatgtcattttgaatcatattactgtgcagGGATACTGCAGGACAGGAGAGATTTCGAAGTCTAATACCAAGTTATATCAGAGATTCTTCTGTTGCTGTAATTGTCTATGATGTTGCAA
attcttttagttatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaatggaacatcaaaatgtccatggaaattctcagcattgtgtatcaaccatgttcattcttttagttatatgtcattttgaatcatattactgtgcagGGATACTGCAGGACAGGAGAGATTTCGAAGTCTAATACCAAGTTATATCAGAGATTCTTCTGTTGCTGTAATTGTCTATGATGTTGCAA
- - - - -catcaaa
- - - - - - - - - - ccatgga
- - - - - - - - - - - - - - -ttctcag
- - - - - - - - - - - - - - - - - - - - - - -tcaacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatcata