Sequence
atgc intronic sequence ATGC exonic sequencegtaagaactttgagcatagccaagccatcttggataatctgatataaaatttcctcaatgtgctggtttttttcccagGATGTACATGAAACTGCAGCAGGAGCTCTATGGAATCTTGCTTTTAATCCTGGTAATGCACTCCGCATTGTTGAGGAAGGAGGAGTTCCAGCTCTTGTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G44900.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G44900.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os10g41360.1 (Oryza sativa), 3'ss of exon 8
--------gtaagaact----ttgagcatag----ccaagccatcttggataat--ctgatataaaatttcctcaatgtgctggtttt----tttcccagGATGTACATGAAACTGCAGCAGGAGCTCTATGGAATCTTGCTTTTAATCCTGGTAATGCACTCCGCATTGTTGAGGAAGGAGGAGTTCCAGCTCTTGTTC
|| | | || ||| | ||| | | || | | ||| || ||| | || || || | ||| || |||||||| || || || || ||||| || ||||||||||||||||| || |||||||||| ||| | |||||||| ||||| || ||||| ||| || |
tgtagattgttatatctatcgttgggaataaatgttttatctgtcattgggaatgaatgctattccttactctagatatgacgactttctgtttattcagGATGTTCACGAGACAGCTGCAGGGGCACTATGGAATCTTGCTTTCTATTCTGGTAATGCTCTCTGTATTGTTGAAGAAGGTGGGGTTCCTATTCTAGTGC
upper sequence: AT2G44900.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G028796_T01 (Zea mays), 3'ss of exon 8
--------------gtaagaactttgagcatagccaagccatcttggataatctgatataaaat-----ttcct----caatgtgctggtttttttcccagGATGTACATGAAACTGCAGCAGGAGCTCTATGGAATCTTGCTTTTAATCCTGGTAATGCACTCCGCATTGTTGAGGAAGGAGGAGTTCCAGCTCTTGTTC
|| || | ||| | |||||| | || || ||||| ||||| || | ||| | |||||||| ||||| || || ||||| || |||||||||||||||||| || |||||||||| |||||||| || || ||||| || || || | ||||||
tattagtatataatagaaagttttcatacttagtacttctgccttggaattggaaacgaaagatgtttgttccttagacaatg-actccctgtttccacagGATGTTCATGAGACAGCTGCAGGGGCACTATGGAATCTTGCTTTTTATTCTGGTAATGCTCTCCGCATAGTCGAAGAAGGTGGGGTGCCTGTTCTTGTAA
upper sequence: AT2G44900.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G079031_T03 (Zea mays), 3'ss of exon 8
-------------gtaagaactttgagcatagccaagccatcttgga---taatctgatataaaatttcct--caatgtgctggttt----ttttcccagGATGTACATGAAACTGCAGCAGGAGCTCTATGGAATCTTGCTTTTAATCCTGGTAATGCACTCCGCATTGTTGAGGAAGGAGGAGTTCCAGCTCTTGTTC
|| || ||||| | |||||| | | | | |||| | | || || ||| | |||||||| || || || || ||||| || |||||||||||||| ||| || |||||||||| |||||||| || || ||||| || ||||| | ||||||
tatagtctataatagaaagttttcatacatagtacttctgccttggagttggaaacaaaaagacatttgttgcttagacaatgattccctgtttccacagGATGTTCACGAGACAGCTGCAGGGGCACTATGGAATCTTGCATTTTATTCTGGTAATGCTCTCCGCATAGTCGAAGAAGGCGGGGTTCCTGTTCTTGTAA
upper sequence: AT2G44900.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA09G37720.1 (Glycine max), 3'ss of exon 9
------------------gtaagaactttgagca---tagccaagccatct-tggataatctgatataaaatttcctcaatgtgctggtttttttcccagGATGTACATGAAACTGCAGCAGGAGCTCTATGGAATCTTGCTTTTAATCCTGGTAATGCACTCCGCATTGTTGAGGAAGGAGGAGTTCCAGCTCTTGTTC
||| ||| | || | | || | || | |||| |||| | | | | | || | |||||||| ||||||||||| |||||||| ||||||||||||||||| ||| || ||||||| || | || || |||||||| ||||| | || ||||||
gttttatatattttgtctgtatacttttttaccatctttatctgtttatatatgtaaaatcctgattaaattcaaactacttttcactttccactttcagGATGTTCATGAAACTGCCGCAGGAGCACTATGGAATCTTGCTTTCAATGCTAGTAATGCTCTAAGAATAGTAGAGGAAGGTGGAGTATCTGCACTTGTTG
upper sequence: AT2G44900.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA18G48840.1 (Glycine max), 3'ss of exon 8
--------------gtaagaactttgagcatagccaagccatcttggataatctg---atataaaatttc--ctcaatgtg--ctggttttt-ttcccagGATGTACATGAAACTGCAGCAGGAGCTCTATGGAATCTTGCTTTTAATCCTGGTAATGCACTCCGCATTGTTGAGGAAGGAGGAGTTCCAGCTCTTGTTC
| ||| | | ||||||| | | | || ||||||| | ||| | |||| | |||||||| ||||||||||| |||||||| ||||||||||| ||||| ||| || | ||||| || | || || |||||||| ||||| | || ||||||
tatatatatattatttttttctttttcctttttctttaccatctttatttgtttatatatgtaaaattctgattaaattcaaaccacttttcactttcagGATGTTCATGAAACTGCCGCAGGAGCACTATGGAATCTGGCTTTCAATGCTAGCAATGCTCTAAGAATAGTAGAGGAAGGTGGAGTATCCGCACTTGTTG
upper sequence: AT2G44900.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv15s0021g01810.t01 (Vitis vinifera), 3'ss of exon 9
------------------------gtaagaactttgagcatagccaagccatcttggataatctgatataaaattt-cctcaatgtgctggtttttttcccagGATGTACATGAAACTGCAGCAGGAGCTCTATGGAATCTTGCTTTTAATCCTGGTAATGCACTCCGCATTGTTGAGGAAGGAGGAGTTCCAGCTCTTGTTC
|| || || | | || | || || ||| | || | | || || | || | | ||| ||||| || ||||| ||||| ||||||||||| ||||||||||| || |||||||||||||| |||||||| || || ||||| ||||| ||||| ||||| |
atgtgatatttgcatcttttatgtttatgacctgttaaaatctctctatattcatg--taaacagaactgattttgaccatgacgta-tatatcctttttcagGACGTCCATGAGACTGCTGCAGGAGCTCTTTGGAATCTTGCCTTCAATCCTGGTAATGCTCTCCGCATAGTGGAAGAAGGGGGAGTGCCAGCCCTTGTCCMapped 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|125257589|gb|EL271674.1|EL271674EST: GTGAAGGTGGGGTTCCACCTCTAATTGCACTTGCACGGTCTGAAGCCGAG GATGTACATGAAACTGCAGCAGGAGCTCTATGGAATCTTGCTT
genomic: GTGAAGGTGGGGTTCCACCTCTAATTGCACTTGCACGGTCTGAAGCCGAGgtaagaactt ... tttttcccagGATGTACATGAAACTGCAGCAGGAGCTCTATGGAATCTTGCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gccatcttggataatctgatataaaatttcctcaatgtgctggtttttttcccagGATGTACATGAAACTGCAGCAGGAGCTCTATGGAATCTTGCTTTTAATCCTGGTAATGCACTCCGCATTGTTGAGGAAGGAGGAGTTCCAGCTCTTGTTC
atctgat putative branch site (score: 4)
ctggtttttttccc putative PPT
ataatctgatataaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaactttgagcatagccaagccatcttggataatctgatataaaatttcctcaatgtgctggtttttttcccagGATGTACATGAAACTGCAGCAGGAGCTCTATGGAATCTTGCTTTTAATCCTGGTAATGCACTCCGCATTGTTGAGGAAGGAGGAGTTCCAGCTCTTGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC