Sequence
atgc intronic sequence ATGC exonic sequencegtaagttctgtttcttattaacttatgtatcatcttttcgtgaatgatgatttagattattaactttgttgtggtgggttttgctgtacagCTTGATGATTGGGTTTTATGTCGAATATACAACAAGAAAGGAACCATGGAGAAGTATTTCCCCGCGGATGAGAAGCCGAGGACCACGACAATGGCTGAAC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G08790.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G08790.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G38560.1 (Glycine max), 3'ss of exon 2
-gtaagttctgtttcttattaacttatgtatcatcttttcgtgaatgatgattta-gattatta---------actttgttgtggtgggttttgctgtacagCTTGATGATTGGGTTTTATGTCGAATATACAACAAGAAAGGAACCATGGAGAAGTATTTCCCCGCGGATGAGAAGCCGAGGACCACGACAATGGCTGAAC
| || || || || || | || | || | | | | || | || ||| ||| | | || || || ||| || || |||||||||||||||||| || |||||||| |||||||||||||| | || ||||| || | | | | | |||| || || | |
tgcaattttaattgtttcccaatcaaa--attagaattgcataagtcttgttctataatttttataaagaaggatctgattttgttgtgttatggtgcacagCTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAGAAATACAACACAGGCGCAGCGAAGATGAATGTTGAGATGGTTCATAGTT
upper sequence: AT5G08790.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G16440.1 (Glycine max), 3'ss of exon 2
------gtaagttctgtttcttattaacttatgtatcatcttttcgtgaatgatgatttagatta---ttaactttgttgtggtgggttttgctgtacagCTTGATGATTGGGTTTTATGTCGAATATACAACAAGAAAGGAACCATGGAGAAGTATTTCCCCGCGGATGAGAAGCCGAGGACCACGACAATGGCTGAAC
|| | || ||| | | | | |||||| || | | |||| || | | | | || || || ||| || || |||||||||||||||||| || |||||||| |||||||||||||| | || ||||| || | | | | |||| || | || |
ttttgattagaaaaggattagaattgcataagttttgatctttcagtttttttttatttttataaaaatggatctgattttgttgtgttatggtgcacagCTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAGAAATACAACACGACCGCACCGAAGATGAATCTTGAAATGATTCATAGTT
upper sequence: AT5G08790.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G32850.1 (Glycine max), 3'ss of exon 2
--gtaagttctgtttcttattaacttatgtatcatcttttcgtg--aatgat----gatttagattattaactttgttgtggtgggttttgctgta-cagCTTGATGATTGGGTTTTATGTCGAATATACAACAAGAAAGGAACCATGGAGAAGTA---TTTCCCCGCGGATGAGAAGCCGAGGACCACGACAATGGCTGAAC
|||| | | | || | || | | || || ||| || ||||| || ||| || ||| ||| | ||| | |||||||||||||||||||| || ||||| |||||||||||||| | || |||||||| | |||| | | | | || | | | | |
gattaagaacagggattaataatgtttcaaagtttggttaggtagaaataatatgtgatttggacaatttttttaactgttgtgcttattggaatggcagCTTGATGATTGGGTTTTGTGCCGAATTTACAACAAGAAAGGGAAGATTGAGAAGTACAATGGTGTTGCGGTGGTGGATCAGAAAGTGGCCAAGTTATCAG---
upper sequence: AT5G08790.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv07s0031g02610.t01 (Vitis vinifera), 3'ss of exon 2
--------gtaagttctgtttcttattaa-----cttatgtatcatcttttcgtgaatgatgattta-gattattaactttgttgtggtgggtttt-----gctgtacagCTTGATGATTGGGTTTTATGTCGAATATACAACAAGAAAGGAACCATGGAGAAGTATTTCCCCGCGGATGAGAAGCCGAGGACCACGACAATGGCTGAAC
|||| |||| | ||||| |||| ||| || | || || | ||| || ||| ||| | || | || | |||||||| |||||||| |||||||||||||||||||||||||| | | ||||| | | || ||| | ||| | | || || ||||
gtacgattgtaa-ttctatactacattaaagatatttatttattatttaaaaaaaaaagaaaaagagtgatggttctttttattgatatatattattattgactttgcagCTTGACGATTGGGTCTTATGTCGAATATACAACAAGAAAGGCAGCGCCGAGAAACAGCACACCTTTGATCAAAAGTCAATGAAATATCCAGAACTTGAAGMapped 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|116381088|gb|EG423680.1|EG423680EST: TCGCTAATGTTGATAGATCAGCTTCTGTTAACAAAAAGAACAACCTACGA CTTGATGATTGGGTTTTATGTCGAATATACAACAAGAAAGGAACCATGGAG
genomic: TCGCTAATGTTGATAGATCAGCTTCTGTTAACAAAAAGAACAACCTACGAgtaagttctg ... tgctgtacagCTTGATGATTGGGTTTTATGTCGAATATACAACAAGAAAGGAACCATGGAG
EST:
gi|125236427|gb|EL250512.1|EL250512EST: TCGCTAATGTTGATAGATCAGCTTCTGTTAACAAAAAGAACAACCTACGA CTTGATGATTG
genomic: TCGCTAATGTTGATAGATCAGCTTCTGTTAACAAAAAGAACAACCTACGAgtaagttctg ... tgctgtacagCTTGATGATTG
EST:
gi|116406839|gb|EG449431.1|EG449431EST: TCGCTAATGTTGATAGATCAGCTTCTGTTAACAAAAAGAACAACCTACGA CTTGATGATTGGGTTTTATGTCGAATATACAACAAGAAAGGAACCATGGAG
genomic: TCGCTAATGTTGATAGATCAGCTTCTGTTAACAAAAAGAACAACCTACGAgtaagttctg ... tgctgtacagCTTGATGATTGGGTTTTATGTCGAATATACAACAAGAAAGGAACCATGGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcgtgaatgatgatttagattattaactttgttgtggtgggttttgctgtacagCTTGATGATTGGGTTTTATGTCGAATATACAACAAGAAAGGAACCATGGAGAAGTATTTCCCCGCGGATGAGAAGCCGAGGACCACGACAATGGCTGAAC
tattaac putative branch site (score: 1)
ttttgct putative PPT
aatgatgatttagatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttctgtttcttattaacttatgtatcatcttttcgtgaatgatgatttagattattaactttgttgtggtgggttttgctgtacagCTTGATGATTGGGTTTTATGTCGAATATACAACAAGAAAGGAACCATGGAGAAGTATTTCCCCGCGGATGAGAAGCCGAGGACCACGACAATGGCTGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC