Sequence
atgc intronic sequence ATGC exonic sequencegtcttacacattttgcttttgctatatacatctctctttttctgtcttgttgaatatcttttatatatatactaagcaatgataactgtatacttcagGTTGCTGCAATAAACACGGCAATGGCAGCTCTTACAAAGACAGTTGGTGTCTTTCCTAAAGAGCGTGCCATAGTGGATAGAGAACGATCCAAAGGGTCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G01320.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G01320.4 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os01g03144.1 (Oryza sativa), 3'ss of exon 7
---------------------------------------------------------------------gtcttaca--cattttgcttttgctatatacatctct-----ctttttctgtcttgttgaatatcttttatatatata-ctaagcaatgataactgtat-acttcagGTTGCTGCAATAAACACGGCAATGGCAGCTCTTACAAAGACAGTTGGTGTCTTTCCTAAAGAGCGTGCCATAGTGGATAGAGAACGATCCAAAGGGTCTT
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gtagaatatgttggattttttatgactcgttgagttgaatttgctaggttgcacatgcttcagattttggacttacattcattctcttcctaatattgactttggtacaagctttttcattgtgtctgagcatttttctgattttgatctgtccctttttcaatttatgagttaagGTAACTGCTATAAACACAGCAATGGCTGCACTGACAAAGACAGTAGGAGTTTTCCCGAAAGAGCGGGCTATAGTTGACAGAGAACGGGCCAAAGGTTCCT
upper sequence: AT2G01320.4 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA20G26160.1 (Glycine max), 3'ss of exon 7
--gtcttacacattttgcttttgctatatacatctctctttttctgtcttgttgaatatcttt---tatatatatactaagcaatgata-actgtatacttcagGTTGCTGCAATAAACACGGCAATGGCAGCTCTTACAAAGACAGTTGGTGTCTTTCCTAAAGAGCGTGCCATAGTGGATAGAGAACGATCCAAAGGGTCTT
| || | | ||||| | | | | || || ||| || || | | | ||| | | || |||||| ||||||||||||| || ||||| ||||| |||||||| |||||||| ||||| || || || || || || ||||||||||| | ||||| || |
acgctttgaaaa----gctttaaacccaaatcttgtgatgttatcaaaatgacaaattcacttggctaagtttgctttccttaattacatggtgagcctcacagGTTACTGCAATAAACACAGCTATGGCTGCTCTCACAAAGACTGTTGGTGTGTTTCCAAAGGAACGGGCAATTGTAGATAGAGAACGTGCTAAAGGCTCAT
upper sequence: AT2G01320.4 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G41110.1 (Glycine max), 3'ss of exon 7
--gtcttacacattttgcttttgctatatacatctctctttttctgtcttgttgaatatcttt---tatatatatactaagcaatgata-actgtatacttcagGTTGCTGCAATAAACACGGCAATGGCAGCTCTTACAAAGACAGTTGGTGTCTTTCCTAAAGAGCGTGCCATAGTGGATAGAGAACGATCCAAAGGGTCTT
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tcgctttgaaa----tgctttaaacccaaatcttgttatgttatcaaaatgacaaattcacttggctaagtttgctttccttaattacatgatgagcctcacagGTTACTGCAATAAACACAGCTATGGCTGCTCTCACAAAGACTGTTGGTGTGTTTCCAAAGGAACGGGCAATTGTAGATAGAGAACGTGCTAAAGGCTCCTMapped 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|86072831|gb|DR368588.1|DR368588EST: GAATGGGGAAGTCTCAGACGTCAATTCAGGACAGAATGGGTTTGCTTCAG GTTGCTGCAATAAACACGGCAATGGCAGCTCTTACAAAGACAGTTGGTGTC
genomic: GAATGGGGAAGTCTCAGACGTCAATTCAGGACAGAATGGGTTTGCTTCAGgtcttacaca ... tatacttcagGTTGCTGCAATAAACACGGCAATGGCAGCTCTTACAAAGACAGTTGGTGTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcttgttgaatatcttttatatatatactaagcaatgataactgtatacttcagGTTGCTGCAATAAACACGGCAATGGCAGCTCTTACAAAGACAGTTGGTGTCTTTCCTAAAGAGCGTGCCATAGTGGATAGAGAACGATCCAAAGGGTCTT
tgataac putative branch site (score: 2)
aatatcttttatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcttacacattttgcttttgctatatacatctctctttttctgtcttgttgaatatcttttatatatatactaagcaatgataactgtatacttcagGTTGCTGCAATAAACACGGCAATGGCAGCTCTTACAAAGACAGTTGGTGTCTTTCCTAAAGAGCGTGCCATAGTGGATAGAGAACGATCCAAAGGGTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA