Sequence
atgc intronic sequence ATGC exonic sequence...caagagagtaactggaaagtggaacataatttcctttattgttcttgcgtttttgttctgctattaccgatgagtaatgttgagattttgtgtgttacagGTGTTCTTTAATCCAGAGATATACAGCAATGACTTCACAACTACTTTACCAGCTGTGATAGACAAATGTATTCAGTCTGCACCAATTGACACACGAAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G13180.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G136662_T01 (Zea mays), 3'ss of exon 5
caagagagtaactggaaagtggaacataat-ttcctttattgttcttgcgtttttgttctgctattacc-gatgagtaatgttgagattttgtgtgt---tacagGTGTTCTTTAATCCAGAGATATACAGCAATGACTTCACAACTACTTTACCAGCTGTGATAGACAAATGTATTCAGTCTGCACCAATTGACACACGAAGAG
| | || | | | || | || || | || ||| | | | ||| || | | | | || | | | | ||| | ||| | ||||| ||||| ||||| ||| || ||| | ||| |||| || | |||| ||||| ||| ||||||||||||||||||||||| | ||||
----taacttgcttgggactaaaagactatgttgatgtacagttggt-catgttttttaggtcagaattaggtgtgcatctctaatcatttaccaacaaatgcagATCTTCTTCAATCCTGAGATTTACTCTGCCGATTTCTCCACTCCTTTGCCCGAGTTGATTGACAACTGTGTTCAGTCTGCACCAATTGACACAAGGAGAG
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G13810.1 (Glycine max), 3'ss of exon 5
---caagagagtaactggaaagtggaacataatttcctttattgttcttgc-gtttttgttctgctattaccgatgagtaatgttgagattttgtgtgttacagGTGTTCTTTAATCCAGAGATATACAGCAATGACTTCACAACTACTTTACCAGCTGTGATAGACAAATGTATTCAGTCTGCACCAATTGACACACGAAGAG
|| || | | || ||| | ||| | ||| | | | | |||| || | ||| || | | || | | || ||| | ||||||||||| |||||||| ||| |||||| || || |||| |||| ||| |||||||| |||||||||||||| |||||||||||| | |||
gtctaatagtggagctaatccatgggtt-cagtttgggtcattatattaacaggacttgtcaaattaacatatatgtgtgttttccccatgatttctg---cagATTTTCTTTAATCCCGAGATATATGGCAGTGACTTTACCACCCCTTTGCCAGTTGTAATAGACAAGTGTATTCAGTCTGCGCCAATTGACACAAGGAGAT
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G13780.1 (Glycine max), 3'ss of exon 5
caagagagtaactggaaagtggaac-ataatttcctttattgttcttgcgttttt--gttctgctatt---accgatgagtaatgttgagattttgtgtgttacagGTGTTCTTTAATCCAGAGATATACAGCAATGACTTCACAACTACTTTACCAGCTGTGATAGACAAATGTATTCAGTCTGCACCAATTGACACACGAAGAG
| |||| | || | | ||| ||| || || || | | | | | | | || || ||| |||| | || | | ||| | ||||||||||| |||||||| || | |||||| || || |||| |||| ||| ||||||||||| ||||||||||| |||||||||||| | |||
-----gtgtaattcctgagctaatctataggttcagttggggtcattatatcaataggaccagtcaatttaacatatctgta-tgttttccctatgatttctgcagATTTTCTTTAATCCTGAGATATATAGTAGTGACTTTACTACCCCTTTGCCAGTTGTAATAGACAAATGCATTCAGTCTGCGCCAATTGACACAAGGAGAT
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G30630.1 (Glycine max), 3'ss of exon 5
---caagagagtaactggaaagtggaacataatttcctttattgttcttgc-gtttttgttctgctattaccgatgagtaatgttgagattttgtgtgttacagGTGTTCTTTAATCCAGAGATATACAGCAATGACTTCACAACTACTTTACCAGCTGTGATAGACAAATGTATTCAGTCTGCACCAATTGACACACGAAGAG
|| | | | || ||| | ||| | || | | | | | || | || | || ||| || | | || | | ||| | ||||||||||| |||||||| ||| |||||| || || |||| |||| ||| |||||||| || ||||||||||| |||||||||||| | |||
gtctaattgtggagctaatccatgggtt-cagtttgggtcataatgttaacaggatcagtcatattaacat--atctgta-tgctttccctatgatttctgcagATTTTCTTTAATCCTGAGATATATGGCAGTGACTTTACCACCCCTTTGCCAGTTGTAATAGACAAGTGCATTCAGTCTGCGCCAATTGACACAAGGAGAT
upper sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv01s0137g00280.t01 (Vitis vinifera), 3'ss of exon 5
caagagagtaactggaaagtggaacataatttcctttattgttcttgcgtttttgttctgctattaccgatgagtaat-gttga--gattttgtgtgtta--cagGTGTTCTTTAATCCAGAGATATACAGCAATGACTTCACAACTACTTTACCAGCTGTGATAGACAAATGTATTCAGTCTGCACCAATTGACACACGAAGAG
| ||| | | | | | || | || || | ||| | | || | | | || || | | ||| || | | ||| ||| | ||||| ||||| ||||| ||||||| || || |||| ||||||||||||| |||||||| ||||||||||||||||||||||||||| |||| |
-----tgtttacttgtgcattgcatttcatctactagatgatgctttgataagtcttttaaaaaaaggaatttgtttttgatgattaatctggctgattatgcagATTTTCTTCAATCCTGAGATCTACAGCAGCGATTTTGCAACCCCTTTACCAGCTGTAATAGACAAGTGTATTCAGTCTGCACCAATTGACACAAGAAGGGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|164103284|gb|ES007148.1|ES007148EST: GTGCACCATACACTTGCGACGTGGGATATGAACGATTCCTTGGACCCGAG GTGTTCTTTAATCCAGAGATATACAGCAATGACTTCACAACTAC
genomic: GTGCACCATACACTTGCGACGTGGGATATGAACGATTCCTTGGACCCGAGgtttgttacc ... tgtgttacagGTGTTCTTTAATCCAGAGATATACAGCAATGACTTCACAACTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcgtttttgttctgctattaccgatgagtaatgttgagattttgtgtgttacagGTGTTCTTTAATCCAGAGATATACAGCAATGACTTCACAACTACTTTACCAGCTGTGATAGACAAATGTATTCAGTCTGCACCAATTGACACACGAAGAG
ttttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caagagagtaactggaaagtggaacataatttcctttattgttcttgcgtttttgttctgctattaccgatgagtaatgttgagattttgtgtgttacagGTGTTCTTTAATCCAGAGATATACAGCAATGACTTCACAACTACTTTACCAGCTGTGATAGACAAATGTATTCAGTCTGCACCAATTGACACACGAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
caagaga
- - - - - - - - - - - aacataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gattttg