Sequence
atgc intronic sequence ATGC exonic sequencegtgagtcatttatgataaaggaagattcttgttcttcttctgctacttctgttgattaataggaatttgattggttggttagCAAAAGAAGAAGATTGTGGATGCTAAGCTTGCAAAGGACTTTCAAGCTGTGTTGAAAGAGTTTCAAAAGGCTCAGCGTCTTGCTGCTGAAAGAGAAACCG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G17730.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G17730.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G33950.1 (Glycine max), 3'ss of exon 2
-----------------gtg-agtcatttatgataaaggaagattcttgttcttcttctgctacttctgttgattaataggaatttgattggttggttagCAAAAGAAGAAGATTGTGGATGCTAAGCTTGCAAAGGACTTTCAAGCTGTGTTGAAAGAGTTTCAAAAGGCTCAGCGTCTTGCTGCTGAAAGAGAAACCG
|| | | | |||| | | || || ||| | | | ||| | ||| ||| | || || |||||||| | ||||| ||||||||||| || ||||| || ||||||||||| ||||| ||||||||||||||| | ||||| || ||||| |
aatgtttgttgtagtttatgtactgaattattagtggcgtgatttttttttcccttgaggaaagaaaaagtgaccttcaatgtcttggttgtatttgcagACAAGTAAGAAGATAGCAGATGCGAAGCTTGCAAAAGATTTTCAGGCGGTGTTGAAAGAATTTCAGAAGGCTCAGCGTCTTTCAGCTGAGAGGGAAACAG
upper sequence: AT4G17730.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G08200.1 (Glycine max), 3'ss of exon 2
-----gtgagtcatttatgataaagg-aagattcttgttcttctt--------------ctgctacttctgttgattaataggaatttgattggttggttagCAAAAGAAGAAGATTGTGGATGCTAAGCTTGCAAAGGACTTTCAAGCTGTGTTGAAAGAGTTTCAAAAGGCTCAGCGTCTTGCTGCTGAAAGAGAAACCG
|||| | || || || || || | || || || || | | ||| ||| | | | |||| | | | |||| |||||||||| |||||||| ||||| || || ||||| || ||||||||||||||||| ||||| || |||||||| ||||| || ||||| |
atactgtgaaa-acttgtgttacgggcaatgtctttattgcattttagggttccatgaccttccatgtcttttgcctcaaaaacatttcttattattgcagGCAAGC-AAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTGTTGAAAGAGTTTCAGAAGGCACAACGTCTTGCAGCTGAGAGGGAAACAG
upper sequence: AT4G17730.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G13410.1 (Glycine max), 3'ss of exon 2
-----gtgagtcattt-----atgataaaggaagattcttgttc---------ttcttctgctacttctgttgattaataggaatttgattggttggttagCAAAAGAAGAAGATTGTGGATGCTAAGCTTGCAAAGGACTTTCAAGCTGTGTTGAAAGAGTTTCAAAAGGCTCAGCGTCTTGCTGCTGAAAGAGAAACCG
|| |||||| |||| || | | |||||| | || | || ||| ||| | | | |||| | || | |||| |||||||| | |||||||| ||||| || || ||||| || ||||||||||||||||| ||||| || |||||||| ||||| || ||||| |
ttaatctgcatcatttttttaatgaaaacagtgaaaacttgttacaggcaatgtctttttagtatgtcttttgcctcaaaaacatttcttatttttgcagGCAAGC-AAGAAGATAGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTGTTGAAAGAGTTTCAGAAGGCACAACGTCTTGCAGCTGAGAGGGAAACAG
upper sequence: AT4G17730.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G01960.1 (Glycine max), 3'ss of exon 2
-----------gtgagtcatttatgataaag----gaagattcttgttcttcttctgctacttctgttgattaataggaatttgattggttg-gttagCA---AAAGAAGAAGATTGTGGATGCTAAGCTTGCAAAGGACTTTCAAGCTGTGTTGAAAGAGTTTCAAAAGGCTCAGCGTCTTGCTGCTGAAAGAGAAACCG
||| | ||| || ||| | ||||| ||| || | | ||| | |||||||| || ||| || |||||||| | ||||| ||||||||||| || ||||| || ||||||||||| ||||| ||||| ||||||||| | || || || ||||| |
agctttatgtactgaattattggtggcgcgatcttgaatttatttgtttttcccttgaggaaagaaaaagtgaccttcaatgt-attggttgtatttgcagGCAAGTAAGAAGATAGCAGATGCGAAGCTTGCAAAAGATTTTCAGGCGGTGTTGAAAGAATTTCAGAAGGCACAGCGTCTTTCAGCGGAGAGGGAAACTG
upper sequence: AT4G17730.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv02s0012g01850.t01 (Vitis vinifera), 3'ss of exon 2
---------gtgagtcatttatgataaaggaagattcttgttcttcttctgctacttctgt------tgattaataggaatttgattggttggttagCAA---AAGAAGAAGATTGTGGATGCTAAGCTTGCAAAGGACTTTCAAGCTGTGTTGAAAGAGTTTCAAAAGGCTCAGCGTCTTGCTGCTGAAAGAGAAACCG
|| || | | | | || ||| ||| | || || || | ||| ||| | | | ||| | |||||||||| |||||||| || ||||| || |||||||| || || ||||||||||| |||||||| || || || || ||||| ||||| |
tttggatatgttagaaaaaggaaacagaagaggatgcttccagtgctgtgatcttttttgaggggtgtaattgccttgaacattctccatctaactgcagGCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTTTTAAAAGAGTTTCAGAAGGCTCAACGGCTGGCAGCAGAAAGGGAAACGGMapped 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|164018635|gb|ES063952.1|ES063952EST: CAGCTAAACTTAAAGAAGCTAGTGAAACTGATCATCAAAGAGGTGCAAAT CAAAAGAAGAAGATTGTGGATGCTAAGCTTGCAAAG
genomic: CAGCTAAACTTAAAGAAGCTAGTGAAACTGATCATCAAAGAGGTGTAAATgtgagtcatt ... ggttggttagCAAAAGAAGAAGATTGTGGATGCTAAGCTTGCAAAG
EST:
gi|164061352|gb|EL992666.1|EL992666EST: CAGCTAAACTTAAAGAAGCTAGTGAAACTGATCATCAAAGAGGTGCAAAT CAAAAGAAGAAGATTGTGGATGCTAAG
genomic: CAGCTAAACTTAAAGAAGCTAGTGAAACTGATCATCAAAGAGGTGTAAATgtgagtcatt ... ggttggttagCAAAAGAAGAAGATTGTGGATGCTAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgttcttcttctgctacttctgttgattaataggaatttgattggttggttagCAAAAGAAGAAGATTGTGGATGCTAAGCTTGCAAAGGACTTTCAAGCTGTGTTGAAAGAGTTTCAAAAGGCTCAGCGTCTTGCTGCTGAAAGAGAAACCG
attaataggaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtcatttatgataaaggaagattcttgttcttcttctgctacttctgttgattaataggaatttgattggttggttagCAAAAGAAGAAGATTGTGGATGCTAAGCTTGCAAAGGACTTTCAAGCTGTGTTGAAAGAGTTTCAAAAGGCTCAGCGTCTTGCTGCTGAAAGAGAAACCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA