Sequence
atgc intronic sequence ATGC exonic sequencegtaatttctcatttgtcatgcttttttctttatagttcccactgaaaaaaattgattggtatggtggtgcaagttttgaggatatatgtgcttctcattgtcgcattctgattctatcttgatttcacaacttttagAATAATGTTGTTGCATCTGGTGGCCTTGGTGGGGAGGTTTTTATATGGGATATTGAAGCTGCTTTGTCACCAGTTACCAAACCTAATGACGCTAATGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G05090.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G05090.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os12g06810.2 (Oryza sativa), 3'ss of exon 5
gtaatttctcatttgtcatgcttttttctttatagttcccactgaaaaaaattgattggtatggtggtgcaagttttgaggatatatgtgcttc-tcattgtcgcattctgattctatcttgatttcacaacttttagAATAATGTTGTTGCATCTGGTGGCCTTGGTGGGGAGGTTTTTATATGGGATATTGAAGCTGCTTTGTCACCAGTTACCAAACCTAATGACGCTAATGAAG
| ||| | | || | || || ||| || || || | | | || | | | || ||| | |||| ||| ||||||| |||||||||||||| || ||||| ||||||||||| |||| || || | | || || ||||| || || || || || |
----------------------------------------------gtatattatccagcactatgctt----ttctgtggaactactcattttatcccttttgttttacatgtttttttttattctctgcaatgtagAGCAATATTGTTGCCTCTGGTGGCCTTGGCGGTGAGGTCTTTATATGGGACCTTGATTCTTCTCTTGCTCCTGTGGCCAAATCTGTAGATGCAAAAGAGG
upper sequence: AT3G05090.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G40440.4 (Glycine max), 3'ss of exon 5
-----gtaatttctcatttgt-catgcttttttctttatagt-tcccactgaaaaaaattgattggtatggtggtgcaagtt-----ttgaggatatatgtgcttc----------tcattgtcgcattc------tgattctatcttgatttcacaacttttagAATAATGTTGTTGCATCTGGTGGCCTTGGTGGGGAGGTTTTTATATGGGATATTGAAGCTGCTTTGTCACCAGTTACCAAACCTAATGACGCTAATGAAG
||| || || |||| | | | |||| | | || ||||| || ||| || | | | | | || | | ||| | ||| ||| |||| || | |||| || | | | || |||||||| ||| ||||||| |||||||||||||||||||||||||||||||||||||| || ||||| | | ||||| | || |||||| | || | |
gtaatgtacttcaaagttcaaacatgttatgcttcttattatgtgccttaagaaaaagttcattttattgtttctatatgctccacattaaacagatagctactttggttgaattatcaatgtcaaatccattctttgatcctttaatagtgtcttgctttttagAACAATATTGTTGCCTCTGGTGGCCTTGGTGGGGAGGTTTTTATATGGGATATCGAGGCTGCCCTCGCTCCAGTCTCTAAGTGTAATGATGATACAGTTG
upper sequence: AT3G05090.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G30050.1 (Glycine max), 3'ss of exon 4
------------------------------------gtaatttctcatttgtcatgcttttttctttatagttcccactgaaaaaaattgat-tggtatggtggtgcaagttttgaggatatatgtgcttctcattgtcgcattctgattctatcttgatttcacaacttttagAATAATGTTGTTGCATCTGGTGGCCTTGGTGGGGAGGTTTTTATATGGGATATTGAAGCTGCTTTGTCACCAGTTACCAAACCTAATGACGCTAATGAAG-
| || | ||||||||| | || || ||| ||| | || || | | | ||| || | || ||| ||| | |||||||||| | | || | ||||||| ||||| ||||| |||||||||||||| |||||| ||||||||||||||||||||||||| | | ||| ||| ||| ||||| | |||| |
gtaatgtgtactatgaacttttcatgcttcttatgaatcgcacaccaagaaaagtttttttttcttcttgtttttatgtgctcaaatatgacatagtttgattg----aatttaaagtttgaat---cttatcaaatccattttctgattctttagaagtgtcgtgaattttagAGCAATGTGGTTGCCTCTGGTGGCCTTGGCGGGGAGATTTTTATATGGGATATTGAAGCTGCACTAGCTTCAGCTACAAAATGCAATGAT-CCAATGGATG
upper sequence: AT3G05090.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G43070.1 (Glycine max), 3'ss of exon 5
gtaattt--ctcatttgtcatgcttttttctttatagttcccactgaaaaa---aattgattggtatggtg-gtgcaagttttgaggatatatgtgcttc----------tcattgtcgcat------tctgattctatcttgatttcacaacttttagAATAATGTTGTTGCATCTGGTGGCCTTGGTGGGGAGGTTTTTATATGGGATATTGAAGCTGCTTTGTCACCAGTTACCAAACCTAATGACGCTAATGAAG---
||||| | || || | || | ||| | | |||| | || |||| | | | | | || | | ||| | ||| ||| | || || | |||| || | | | || |||||||| ||| |||||| |||||||||||||||||||||||||||||||||||||| || ||||| | | || | || |||||| |||| | |
gtaatgtactccaaacatcttatgcttcttattaagtgtatcgagaaaaagttcattttattgtttctatatgctccacattgaaacagatagctactttggttgaattatcaatttcaaatccattctttgatcctttaatagtgtcttgctttttagAACAATACTGTTGCCTCTGGTGGCCTTGGTGGGGAGGTTTTTATATGGGATATCGAGGCTGCCCTTGCTCC---CTCTAAGTGTAATGATGCTATGGTTGATG
upper sequence: AT3G05090.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G40360.1 (Glycine max), 3'ss of exon 5
gtaatttctcatttgtcatgct-tttttctttatagttcccactgaaaaaaattgattggtatggtggtgcaagtt-----ttgagg-atatatgtgcttc-----------------tcattgtcgcattc------tgattctatcttgatttcacaacttttagAATAATGTTGTTGCATCTGGTGGCCTTGGTGGGGAGGTTTTTATATGGGATATTGAAGCTGCTTTGTCACCAGTTACCAAACCTAATGACGCTAATGAAG
||||| | | |||| | | ||||| || | | | ||||| || ||| || | | | ||| ||||| | ||| | ||| | |||| || | |||| | | | | ||| ||||||| ||| ||||||| |||||||||||||| ||||||||||||||||||||||| || ||||| | | ||||| | || ||||| |||| | |
gtaatgtact-tcaatcatcttatgcttcttattaagtgcatcaagaaaaagttcattttattgtttttatacgttccacattgagtcagatagatactttggttgaattatcagtatcaactgtcaaatccattatttgatcgtttaatagtgtcatgcattttagAGCAATATTGTTGCCTCTGGTGGCCTTGGCGGGGAGGTTTTTATATGGGATATCGAGGCTGCCCTCACTCCAGTCTCTAAGTGCAATGATGCTACAGTTG
upper sequence: AT3G05090.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G42990.1 (Glycine max), 3'ss of exon 5
gtaattt--ctcatttgtcatgcttttttctttatagttcccactgaaaaaaattgattggtatggtggtgcaagtt-----ttgag---gatatatgt--------gcttctcattgtcg-------catt--ctgattctatcttgatttcacaacttttagAATAATGTTGTTGCATCTGGTGGCCTTGGTGGGGAGGTTTTTATATGGGATATTGAAGCTGCTTTGTCACCAGTTACCAAACCTAATGACGCTAATGAAG
||||| | ||| || | || | ||| | || ||||||| || ||| || | | | ||| ||||| |||| | || ||| | ||| |||| |||| | | | | ||| ||||||| ||| ||||||| |||||||||||||| ||||||||||||||||||||||| || ||||| | | || ||| | || ||||| |||| |
gtaatgtacttcaaacatcttatgcttcttattaagtgtgtcaa-gaaaaaagttcattttattgtttttatacgttccacattgagtcagatagaaactttggttgaattatcagtatcgtcaaatccattatttgatcgtttaatagtgtcatgcattttagAGCAATATTGTTGCCTCTGGTGGCCTTGGCGGGGAGGTTTTTATATGGGATATCGAGGCTGCCATCACTCCGGTTTCTAAGTGCAATGATGCTACAATTG
upper sequence: AT3G05090.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv14s0030g01350.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------gtaatttctcatttgtcatgcttttttctttatagttcc--cactgaaaaaaattgattggtatggtggtgcaagttttgaggatatatgtg----cttctcattgtcgcattctgattctatcttgatttcacaacttttagAATAATGTTGTTGCATCTGGTGGCCTTGGTGGGGAGGTTTTTATATGGGATATTGAAGCTGCTTTGTCACCAGTTACCAAACCTAATGACGCTAATGAAG-
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gtaatttctttgtcaaaattttcatggaattatttactgcatagatgaagggttcttgtcagtgtaatgctgttatttaagtttcatgttcaatttaatggtgcatatttgggggcattgtgtcatattttgtcgttatcattttctgatccttttatagtgtcatgcattttagAGCAATGTTGTTGCCTCTGGTGGCCTTGGTGGGGAGGTTTTTGTATGGGATCTGGAAGCTGCACTAACTCCAGTCTCAAAGTCAAGTGATGC-AATGGAGGMapped 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|116449111|gb|EG491703.1|EG491703EST: TCCGTCAGCATTCTGACTATGTTACTTGTTTGGCAGTTGCGGCAAAAA-T AATAATGTTGTTGCATCTGGTGGCCTTG
genomic: TCCGTCAGCATTCTGACTATGTTACTTGTTTGGCAGTTGCGGCAAAAAATgtaatttctc ... caacttttagAATAATGTTGTTGCATCTGGTGGCCTTG
EST:
gi|116407303|gb|EG449895.1|EG449895EST: TCCGTCAGCATTCTGACTATGTTACTTGTTTGGCAGTTGCGGCAAAAAAT AATAATGTTGTTGCATCTGGTGGCCTTGGTGG
genomic: TCCGTCAGCATTCTGACTATGTTACTTGTTTGGCAGTTGCGGCAAAAAATgtaatttctc ... caacttttagAATAATGTTGTTGCATCTGGTGGCCTTGGTGG
EST:
gi|116407307|gb|EG449899.1|EG449899EST: TCCGTCAGCATTCTGACTATGTTACTTGTTTGGCAGTTGCGGCAAAAAAT AATAATGTTGTTGCATCTGGTGGCCTTGGTGGGGAGGTTTTTATATGGGAT
genomic: TCCGTCAGCATTCTGACTATGTTACTTGTTTGGCAGTTGCGGCAAAAAATgtaatttctc ... caacttttagAATAATGTTGTTGCATCTGGTGGCCTTGGTGGGGAGGTTTTTATATGGGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatatgtgcttctcattgtcgcattctgattctatcttgatttcacaacttttagAATAATGTTGTTGCATCTGGTGGCCTTGGTGGGGAGGTTTTTATATGGGATATTGAAGCTGCTTTGTCACCAGTTACCAAACCTAATGACGCTAATGAAG
ctttt CT-rich tract
aactttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttctcatttgtcatgcttttttctttatagttcccactgaaaaaaattgattggtatggtggtgcaagttttgaggatatatgtgcttctcattgtcgcattctgattctatcttgatttcacaacttttagAATAATGTTGTTGCATCTGGTGGCCTTGGTGGGGAGGTTTTTATATGGGATATTGAAGCTGCTTTGTCACCAGTTACCAAACCTAATGACGCTAATGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT