Sequence
atgc intronic sequence ATGC exonic sequencegtaaactctattatgatccaaactaggcttgatgtatgtagttgagaaatgtgtttctgtttgaatcttacaactggttataatttgagcagCACAAGGTCAAGATCTGAGCAGTCACTGGTTCGATGGGCGACACCACAACTTCACGACATTGATGCTTTAGCCAAAATGGTTGATCCAGCTCTTAAAGGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G53730.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G53730.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA19G45130.1 (Glycine max), 3'ss of exon 14
-----------------gtaaactctattatgatccaaactaggcttgatgtatgtagttgagaaatgtgtttctgtttgaatctta-caactggttataa----tttga--gcagCACAAGGTCAAGATCTGAGCAGTCACTGGTTCGATGGGCGACACCACAACTTCACGACATTGATGCTTTAGCCAAAATGGTTGATCCAGCTCTTAAAGGG
| | ||| | | | || | | | | || || | || | ||| || | ||| || || || | |||| ||||| |||||||||||||||| ||||||||||||| ||||| ||||| || || |||||||| || || |||||||||||||| || | ||||||
gtgaattaatggttttctttatgtctgctctcacgtttttgagcaatattctgcagattttgaaattatgcacaaataataatgttgtctcctgattgcaaaacattccatgacagCTCAAGGCCAAGATCTGAGCAGTCTTTGGTTCGATGGGCAACACCTCAACTCCATGATATTGATGCATTGGCTAAAATGGTTGATCCTGCAATGAAAGGG
upper sequence: AT1G53730.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA03G42360.1 (Glycine max), 3'ss of exon 16
--------gtaaactctattatgatccaaactagg---cttgatgtatgtagttgagaaatgtgtttctgtttgaatcttacaa---------ctggttataa-----tttg-agcagCACAAGGTCAAGATCTGAGCAGTCACTGGTTCGATGGGCGACACCACAACTTCACGACATTGATGCTTTAGCCAAAATGGTTGATCCAGCTCTTAAAGGG
| | | || || || || |||| || | | |||||| || | | | || | | || ||| || | | || | |||| ||||| |||||||||||||||| ||||||||||||| ||||| ||||| || || |||||||| || || |||||||||||||| || | ||||||
gtgaattaatggttttttttttggtctgctctcacgtttttgagcaatattctgcagaaat-tgaaattatgtagatataataatgttgtctcctgattgcgaaacattctgtaacagCTCAAGGCCAAGATCTGAGCAGTCTTTGGTTCGATGGGCAACACCTCAACTCCATGATATTGATGCATTGGCTAAAATGGTTGATCCTGCAATGAAAGGG
upper sequence: AT1G53730.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA16G01790.1 (Glycine max), 3'ss of exon 14
-----------gtaaactctattatgatccaaactaggctt---gatgtatgtagttgagaa-----atgtgtttctgtttgaatcttacaactggttataatttgagcagCACAAGGTCAAGATCTGAGCAGTCACTGGTTCGATGGGCGACACCACAACTTCACGACATTGATGCTTTAGCCAAAATGGTTGATCCAGCTCTTAAAGGG
|| | | || || | | ||| ||||| | || || ||| | || ||| | ||| ||| | || |||| ||||| | || ||||||||| | ||||||||||||| ||||| ||||| || || || |||||||| || |||||||||||||| || | ||||
gtaagattgatatacctttaagtagcataacagttttacttttacatgtacacactttcaaacattaatgggcacatgcatgattgttaaaac-----gttccttctacagCTCAAGGCCGAGGTCTGAGCAGGCGTTGGTTCGATGGGCAACACCTCAACTCCATGATATCGATGCTTTGGCTAAAATGGTTGATCCTGCATTGGAAGGA
upper sequence: AT1G53730.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA07G05230.1 (Glycine max), 3'ss of exon 14
-------------gtaaactctattatgatccaaactaggcttg---atgtatgtagttg-----agaaatgtgtttctgtttgaatcttacaactggttataatttgagcagCACAAGGTCAAGATCTGAGCAGTCACTGGTTCGATGGGCGACACCACAACTTCACGACATTGATGCTTTAGCCAAAATGGTTGATCCAGCTCTTAAAGGG
|| | | || || | | ||| ||||| | || | ||||| | || ||| | ||| ||| ||| || |||| ||||| | || ||||||||| | ||||||||||||| ||||| ||||| ||||| || ||||| | || |||||||||||||| | | ||||
gtgaaagattgatatacctttaagtaacataacagttttacttttacatgtacacactttcaaacataaatgggcacatgcctgattgttaaaac--gttccttctt---cagCTCAAGGCCGAGGTCTGAGCAGGCTTTGGTTCGATGGGCAACACCTCAACTCCACGATATCGATGCCCTGGCTAAAATGGTTGATCCTACATTGGAAGGA
upper sequence: AT1G53730.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv09s0002g00150.t01 (Vitis vinifera), 3'ss of exon 14
----------------gtaaactctattatgatccaa--actaggcttgatgtatgtag---ttgagaaatgtgtttctgtttgaatcttacaactg-gttataatttg--agcagCACAAGGTCAAGATCTGAGCAGTCACTGGTTCGATGGGCGACACCACAACTTCACGACATTGATGCTTTAGCCAAAATGGTTGATCCAGCTCTTAAAGGG
| | | ||||| | | || |||| | || ||| || || | | | || || | | |||| |||| |||| | ||||| ||||||||||| || ||||||||||||| || || || ||||| ||||| |||||| | || |||||||||||||| || || ||||||
gtaaaaatgttgcactactagccatccaatgattccattaccttttttgaagagaaaaggacctgaatcataccattttctacttagctaactattatgttaacattttctgacagCTCCAGGTCCAGATCTGAGCAATCTTTGGTTCGATGGGCTACTCCTCAGCTTCATGACATCGATGCTCTGGCTAAAATGGTTGATCCGGCACTCAAAGGGMapped 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|125171263|gb|EL194245.1|EL194245EST: GAAAACCATTTTGACAG CACAAGGTCAAGATCTGAGCAGTCACTGGTTCGATGGGCGACACCACAAC
genomic: GAAAACCA-TTTGACAGgtaaactcta ... atttgagcagCACAAGGTCAAGATCTGAGCAGTCACTGGTTCGATGGGCGACACCACAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtagttgagaaatgtgtttctgtttgaatcttacaactggttataatttgagcagCACAAGGTCAAGATCTGAGCAGTCACTGGTTCGATGGGCGACACCACAACTTCACGACATTGATGCTTTAGCCAAAATGGTTGATCCAGCTCTTAAAGGG
atcttac putative branch site (score: 3)
ttataatttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaactctattatgatccaaactaggcttgatgtatgtagttgagaaatgtgtttctgtttgaatcttacaactggttataatttgagcagCACAAGGTCAAGATCTGAGCAGTCACTGGTTCGATGGGCGACACCACAACTTCACGACATTGATGCTTTAGCCAAAATGGTTGATCCAGCTCTTAAAGGG
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