Sequence
atgc intronic sequence ATGC exonic sequence...gaatgatatcttccttggagataacagtttgcagtgaatctattttgcaccgatcagaaaagagtagctttgtgaatttttatttcatgtttcattacagATTGCAACTGGAGGAGGGGGTGGAAACATTGGAAAGAGTATCAATAATGGTGGTGGCGATGGAGGTGACGATAATGGTGATGATGATGATTACTTTGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G24690.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G24690.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os12g18630.1 (Oryza sativa), 3'ss of exon 1
-gaatgatatcttccttggagataacagtttgc-agtgaatctattttgc-accgatcagaaaagagtagctttgtgaatttttatttcatgtttcattacagATTGCAACTGGAGGAGGGGGTGGAAACATTGGAAAGAGTATCAATAATGGTGGTGGCGATGGAGGTGACGATAATGGTGATGATGATGATTACTTTGATG
|| || | || | || | | | | ||| || | | | | | | | || | || ||| | | || ||| | ||||| || || || ||||| | ||||| || || || | |||||||||| ||||| || || ||| |||| ||||||||||||||||||||||
caaaatatctgttattccatcgtactgccatattaatttgtgagtttgatgactggattgcatatattcatcatatgcctcttcttttaaaat---gttgcagCTGGCAACAGGTGGTGGCGGTGGTGATATTGGGAAAAGGATTGGTCATGGTGGTGGTGATGGTGGAGATGATGATGGCGATGATGATGATTACTTTGATG
upper sequence: AT5G24690.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA15G05240.1 (Glycine max), 3'ss of exon 1
----gaatgatatcttccttggagataacagtttgcagtgaatctattttgcaccgatcagaaaagagtagctttgtgaatttttatttcatgtttc---attacagATTGCAACTGGAGGAGGGGGTGGAAACATTGGAAAGAGTATCAATAATGGTGGTGGCGATGGAGGTGACGATAATGGTGATGATGATGATTACTTTGATG
|| | | |||||| || | || |||||| | | || | ||| || ||| | ||||||| || || ||| | | | ||| ||||| || ||| |||||||||||| |||||| |||||||||| ||||||||||| ||| |||| |||||||| |||||||||||||
aatgacatcgtgtagtccttgtagctgacttcacttagtgaaataaagattcatttgttgt-------tagtatttggaaatccattttcatgcttttaatttgcagCTAGACATTGGGGGAGGTGGAGGAGACATTGGAAAGAAAATCAATCATGGTGGTGGTGATGGAGGTGATGATGATGGGGATGATGACGATTACTTTGATG
upper sequence: AT5G24690.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G19780.1 (Glycine max), 3'ss of exon 1
gaatgatatcttccttggagataaca-gtttgcagtgaatctattttgcaccgatcagaaaagagtagctttgtgaatttttattt-catg--tttcattacagATTGCAACTGGAGGAGGGGGTGGAAACATTGGAAAGAGTATCAATAATGGTGGTGGCGATGGAGGTGACGATAATGGTGATGATGATGATTACTTTGATG
| | || | | | | || | || | || || ||| | | | || | || | || |||| |||| ||| || ||| | | | ||| ||||| || ||| | || ||||||| |||||| |||||||||| ||||||||||| ||| |||| || ||||| |||||||||||||
---tttaagtttgcccaatggcatcgtgtagcccatgtagctgactt-cacttgttgttagtatttgcctatttggaaattcattttcatgcttttgtttgcagCTAGACATTGGGGGAGGTGGGGGAGATATCGGAAAGAAAATCAATCATGGTGGTGGTGATGGAGGTGATGATGATGGGGACGATGACGATTACTTTGATG
upper sequence: AT5G24690.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S309_83V6.1 (Physcomitrella patens), 3'ss of exon 1
gaatgatatcttc-cttggagataac--agtttgcagtgaatctattttgcaccgatcagaaaagagtagctttgt-gaatttttatttcatgtttcattacagATTGCAACTGGAGGAGGGGGTGGAAACATTGGAAAGAGTATCAATAATGGTGGTGGCGATGGAGGTGACGATAATGGTGATGATGATGATTACTTTGATG
| || ||| ||| | | | || || || ||||| | || | | | | || | | | | || | | ||| | | | ||| || || |||||| |||||||| | | |||||| ||||| ||||||||||||||| |||| || |||||||| ||||| | ||
--cttatcctttcgcttaaatgtgatctaggttctgcgtttggtaatttgcgtaggtctaagttggtcaaggtggttggaatggcaacgtttgggtg--tgcagGTGGAACTTGGTGGTGGTGGTGGAGGTATTGGAAATAAGAATTTTAATGGGGGTGGTGATGGAGGTGACGATGATGGCGACGATGATGACTACTTCGGTG
upper sequence: AT5G24690.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S4_62V6.2 (Physcomitrella patens), 3'ss of exon 1
--gaatgatatcttccttggagataacagtttgcagtgaatctat-tttgcaccgatcagaaaagagtagctttgtgaatttttatttcatgtttcattacagATTGCAACTGGAGGAGGGGGTGGAAACATTGGAAAGAGTATCAATAATGGTGGTGGCGATGGAGGTGACGATAATGGTGATGATGATGATTACTTTGATG
| || || |||| | ||||| | | | | || |||| | | | | || | || | || || | ||| || || | | ||||| || || ||| ||||| || | | | ||||| |||||||| |||||||||||| ||||||||||||| || ||||||| ||
gtggatagcctcaacctttg-gataaggttaacctacggttttaggtttggagtcacttggctcgc-tatttgcttggaattg-atgacgattttggttgtagGTGGAGCTCGGAGGTGGTGGCGGAGGAATTGGTAATAAGAACTTCAATGGGGGTGGCGACGGAGGTGACGATGATGGTGATGATGACGACTACTTTGGTGMapped 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|124732850|gb|EH824252.1|EH824252EST: TATGACCCAGAAGATTTCTGAGACTAGCCCTGAG ATTGCAACTGGAGGAGGGGGTGGAAACATTGGAAAGAGTATCAATAATGGG
genomic: TATGACCCAGAAGATTTCTGAGACTAGCCCTGAGgtctctctct ... ttcattacagATTGCAACTGGAGGAGGGGGTGGAAACATTGGAAAGAGTATCAATAATGG-
EST:
gi|124947372|gb|EL023215.1|EL023215EST: TGACCCAGAAGATTTCTGAGACTAGCCCTGAG ATTGCAACTGGAGGAGGGGGTGGAAACATTGGAAAGAGTATCAA
genomic: TGACCCAGAAGATTTCTGAGACTAGCCCTGAGgtctctctct ... ttcattacagATTGCAACTGGAGGAGGGGGTGGAAACATTGGAAAGAGTATCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcaccgatcagaaaagagtagctttgtgaatttttatttcatgtttcattacagATTGCAACTGGAGGAGGGGGTGGAAACATTGGAAAGAGTATCAATAATGGTGGTGGCGATGGAGGTGACGATAATGGTGATGATGATGATTACTTTGATG
tttcatt CT-rich tract
aatttttatttcatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaatgatatcttccttggagataacagtttgcagtgaatctattttgcaccgatcagaaaagagtagctttgtgaatttttatttcatgtttcattacagATTGCAACTGGAGGAGGGGGTGGAAACATTGGAAAGAGTATCAATAATGGTGGTGGCGATGGAGGTGACGATAATGGTGATGATGATGATTACTTTGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - -gataaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - cagaaaa