Sequence
atgc intronic sequence ATGC exonic sequencegtattattaagcaatcgtgctctgtgaaaggactttcataaatctcttgttgattattgaaatttccaagttctctctgcctttcagAAAGAACTTGCACAGCTTACATGTGAATGTGAAAGACACATTGGAACACAATCTGGTGGGATGGACCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G06580.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G06580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G47350.1 (Glycine max), 3'ss of exon 4
-------------------gtattattaagcaatcgt-gctctgtgaaaggactttcataaatctcttgttgat-tattgaaatttccaagttctctctgcctttcagAAAGAACTTGCACAGCTTACATGTGAATGTGAAAGACACATTGGAACACAATCTGGTGGGATGGACCAG
|| | | || | | | | || || | ||| |||| | | ||| || || | | ||| | ||| | | ||||||||| ||||||| ||||| ||||||||||||||| ||||||||||||||||||| || ||||| |||
accttttgcataaagtgacaaatgaccagaggattattggtgtttggaatgcattttataa-tttaacgttcatgtacttacattcatatgttgt-------tgacagAAAGAAATTGCACAACTTACGTGTGAATGTGAAAGATACATTGGAACACAATCTGGAGGAATGGATCAG
upper sequence: AT3G06580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G03990.1 (Glycine max), 3'ss of exon 5
------------gtattattaagcaat-cgtg-ctctgtgaaaggactttcataaatctcttgttgattattgaaatttccaagttctctctgcctttcagAAAGAACTTGCACAGCTTACATGTGAATGTGAAAGACACATTGGAACACAATCTGGTGGGATGGACCAG
|| | ||| ||| | | || | ||||| ||| || | | | || || ||| | | | | | | | ||||||||||||||||| |||||||||| |||||| |||| ||||| || ||||||||||||||||| |||
caatttactacagtgcttttattgaatgcatctctttttgaaaaatattttattgttgtttattttgtttctgacacaaatta-tcatatattgttgacagAAAGAACTTGCACAAGTTACATGTGATTGTGAACGACATATTGGGACTCAATCTGGTGGGATGGATCAG
upper sequence: AT3G06580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G36610.1 (Glycine max), 3'ss of exon 5
gtattattaagca-atcgtgctctgtgaaagg----actttcataaatct----cttgttgattattgaaatttc--caagttctc---tctgcctttcagAAAGAACTTGCACAGCTTACATGTGAATGTGAAAGACACATTGGAACACAATCTGGTGGGATGGACCAG
| ||||| | | ||| | || ||| | | | | | | || ||| ||||| || ||| || || | | | ||||||||||||||||| |||||||||| |||||| |||| ||||| || ||||||||||||||||| |||
-ttttattgaatacatctctttttgaaaaatattctattgttgtttgtttaatattttttgtttattctgtttctgacaaattatcatattttgttgacagAAAGAACTTGCACAAGTTACATGTGATTGTGAACGACATATTGGGACTCAATCTGGTGGGATGGATCAG
upper sequence: AT3G06580.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv05s0077g00690.t01 (Vitis vinifera), 3'ss of exon 5
--------gtattattaagcaatcgtgctctgtgaaaggactt--tcata-aatctcttgt--tgattattgaaatttccaagttctctctgcctttcagAAAGAACTTGCACAGCTTACATGTGAATGTGAAAGACACATTGGAACACAATCTGGTGGGATGGACCAG
| | | || ||| | | ||| |||| ||| | | | || || | | | | || || ||||||||||| |||| || || |||||||||||||| ||||||||||||||||||||||||| |||||||||
tacagggaatggcctaagctaaattggcttcatttattagcttgaccatacaatagcaaatcctatttgtttattctaatatttgttccttgtttttcagAAAGACGTTGCCCAACTAACATGTGAATGTGAGCGACACATTGGAACACAATCTGGTGGTATGGACCAGMapped 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|125124914|gb|EL170614.1|EL170614EST: CAACAATTGCTATTATGGCTGTCTTTGGTCATAACTTTGAGAAG AAAGAACTTGCACAGCTTACATGTGAATGTGAAAGACACATTGGAACACAA
genomic: CAACAATTGCTATTATGGCTGTCTTTGGTCATAACTTTGAGAAGgtattattaa ... tgcctttcagAAAGAACTTGCACAGCTTACATGTGAATGTGAAAGACACATTGGAACACAA
EST:
gi|124740007|gb|EH831169.1|EH831169EST: GCTCAGCAACAATTGCTATTATGGCTGTCTTTGGTCATAACTTTGAGAAG AAAGAACTTGCACAGCTTACATGTGAA
genomic: GCTCAGCAACAATTGCTATTATGGCTGTCTTTGGTCATAACTTTGAGAAGgtattattaa ... tgcctttcagAAAGAACTTGCACAGCTTACATGTGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttcataaatctcttgttgattattgaaatttccaagttctctctgcctttcagAAAGAACTTGCACAGCTTACATGTGAATGTGAAAGACACATTGGAACACAATCTGGTGGGATGGACCAG
tgttgat putative branch site (score: 4)
ttctctctgcctttc putative PPT
ttgattattgaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattattaagcaatcgtgctctgtgaaaggactttcataaatctcttgttgattattgaaatttccaagttctctctgcctttcagAAAGAACTTGCACAGCTTACATGTGAATGTGAAAGACACATTGGAACACAATCTGGTGGGATGGACCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA