Sequence
atgc intronic sequence ATGC exonic sequencegtaagtagatagatgcagaattgtatctttttcttttcaacaccgggtggatattctgctgctttggtgctatgatgtatcaattgttcgattcagtaaagaacatgggacgtgagcctacatcatgatgccattgactgtgattaattggaatctcagttttgcagGAGCACCTGTTAATAGTATGTGAACTTCTCAAGGCAAACTTGTATGAGTTCCAAAAGTTTAATAGGGAATCAGGGGGAGAGGTTTATTTCACTATGCCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G17750.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G17750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G015073_T01 (Zea mays), 3'ss of exon 3
gtaagtagatagatgcagaattgtatctttttcttttcaacaccgggtggatattctgctgctttggtgctatgatgtatcaattgttcgattcagtaaagaacatgggacgtgagcctacatcatgatgccattgactgtgattaattggaatctcagttttgcagGAGCACCTGTTAATAGTATGTGAACTTCTCAAGGCAAACTTGTATGAGTTCCAAAAGTTTAATAGGGAATCAGGGGGAGAGGTTTATTTCACTATGCCAA
| || | ||| | | ||||| | || || || || | | | ||| ||| || || ||| || ||| ||||||||| || || | ||||| ||||||||||| |||||||| |||||||||| || || || || || ||||||||||| |||||||| ||||| |||||||
---------------------------------------------------------ggaatttcagagctcagggttgataattggttcttttccaaagcaatttgc--cttaaagtcacaacat----ttctttaccac--ttatttcaaatactg--tttgcagGAACATTTGCTGATAGTCTGTGAACTTCTGAAGGCAAATCTGTATGAGTTTCAGAAATTCAACAGAGAATCAGGGGGTGAGGTTTACTTCACAATGCCAA
upper sequence: AT3G17750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G181002_T01 (Zea mays), 3'ss of exon 3
gtaagtagatagatgcagaattgtatctttttcttttcaacaccgggtggatattctgctgctttggtgctatgatgtatcaattgttcgattcagtaaagaacatgggacgtgagcctacatcatgatgccattgactgtgattaattggaatctcagttttgcagGAGCACCTGTTAATAGTATGTGAACTTCTCAAGGCAAACTTGTATGAGTTCCAAAAGTTTAATAGGGAATCAGGGGGAGAGGTTTATTTCACTATGCCAA
| | | | | | ||||| || || | | ||| | | | | || | | | ||| ||| || || | |||||||||||| || | ||||| ||||||||||| |||||||| |||| ||||| || || || || || ||||||||||| |||||||| ||||| |||||||
-----------------------------------------------------------taaatgactcttctccaaaacaaattgctc---tcgagtcacagcatcatataataaagtttgttgtgtttgctgt-actac--ttattttaaacattg--tttgcagGAGCATTTGCTGATAGTCTGTGAACTTCTGAAGGCAAATCTGTACGAGTTTCAGAAATTCAACAGAGAATCAGGGGGTGAGGTTTACTTCACAATGCCAA
upper sequence: AT3G17750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 3
gtaagtagatagatgcagaattgtatctttttcttttcaacaccgggtggatattctgctgctttggtgctat-gatgtatcaattgttcgattcagtaaagaacatgggacgtgagcctacatcatgatgccattgactgtgattaattggaatctca--gttttgcagGAGCACCTGTTAATAGTATGTGAACTTCTCAAGGCAAACTTGTATGAGTTCCAAAAGTTTAATAGGGAATCAGGGGGAGAGGTTTATTTCACTATGCCAA
||| | || | || | | ||| | || | | || | | | || | | | || | | | | | | || || || || | |||||| || ||||||||||||||||||| || || ||||||||||||||||| || || |||||||| |||||||| || || || || || || |||||||
-------------------------------------------------------------gtttacttctgttaatttttgaatggccttgtttatt------tatagttc-tacaccaaatttgtcatctaact--ttatcactctttcttttcccattgtatggcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA
upper sequence: AT3G17750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 5
gtaagtagatagatgcagaattgtatctttttcttttcaacaccgggtggatattctgctgctttggtgctatgatgtatcaattgttcgattcagtaaagaacatgggacgtgagcctacatcatgatgccattgactgtgattaattggaatctca--gttttgcagGAGCACCTGTTAATAGTATGTGAACTTCTCAAGGCAAACTTGTATGAGTTCCAAAAGTTTAATAGGGAATCAGGGGGAGAGGTTTATTTCACTATGCCAA
|| | | | | |||| || || | | | | | || || | | || ||| | | | || || || || | ||||||||| |||||||||||||||| || || || ||||||||||||||||| || || |||||||| |||||||| || || || || || || |||||||
-------------------------------------------------------------------tgtttacttctgttaattttttaatgccttgtttattaatagttgtacaccaaatttgccatctgatt--tcatcactctttcttttcccattgtatggcagGAGCATTTGTTAATAGTATGTGAGCTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA
upper sequence: AT3G17750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G29970.1 (Glycine max), 3'ss of exon 3
gtaagtagatagatgcagaattgtatctttttcttttcaacaccgggtggatattctgctgctttggtgctatgatgtatcaattgttcgattcagtaaagaacatgggacgtgagcctacatcatgatgccattgactgtgattaattggaatctcagttttgcagGAGCACCTGTTAATAGTATGTGAACTTCTCAAGGCAAACTTGTATGAGTTCCAAAAGTTTAATAGGGAATCAGGGGGAGAGGTTTATTTCACTATGCCAA
|| ||| | || ||| | | | | || | | || || || | || | | || || ||| ||| | | | || ||||||| || ||||||||||||||||||| || || || ||||| |||||||| || || |||||| | ||||||||||| || || |||||||| |||||||
----------------------------------------------------------atgttttaaaac-attatg-aggggctatccttttaaactatgatgttgagaaata--tctgtttactagtg--atcatctgactttactacg---ccttgtactgcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCCAACTTATATGAGTTTCACAAATTTAATCGAGAATCAGGGGGTGAAGTGTATTTCACGATGCCAA
upper sequence: AT3G17750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G34510.1 (Glycine max), 3'ss of exon 3
gtaagtagatagatgcagaattgtatctttttcttttcaacaccgggtggatattctgctgctttggtgctatgatgtatcaattgttcgattcagtaaagaacatgggacgtgagcctacatcatgatgccattgactgtgattaattggaatctca-gttttgcagGAGCACCTGTTAATAGTATGTGAACTTCTCAAGGCAAACTTGTATGAGTTCCAAAAGTTTAATAGGGAATCAGGGGGAGAGGTTTATTTCACTATGCCAA
|||| | | || | | || || | | || || | ||| | ||| | || | ||| || ||||||| || ||||||||||||||||||| || || || || || |||||||| || || |||||| | ||||||||||| || || |||||||| |||||||
-----------------------------------------------------------------aacataatgaagggctatccttttaa---actataggcaaagtgatgttgagaaatatctgttgattagtgatcatctgactttactacctcttgtactgcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCCAATTTATATGAGTTTCACAAATTTAATCGAGAATCAGGGGGGGAAGTGTATTTCACGATGCCAA
upper sequence: AT3G17750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 9
gtaagtagatagatgcagaattgtatctttttcttttcaacaccgggtggatattctgctgctttggtgctatgatgtatcaattgttcgattcagtaaagaacatgggacgtgagcctacatcatgatgccattgactgtgattaattggaatctcagttttgcagGAGCACCTGTTAATAGTATGTGAACTTCTCAAGGCAAACTTGTATGAGTTCCAAAAGTTTAATAGGGAATCAGGGGGAGAGGTTTATTTCACTATGCCAA
|| ||| | || | ||| || || | | | || || | | | | | |||| | || | | || | | ||| || || |||||||||| || | ||||| ||||| ||||||||||||||||||||||||||||| || || |||||||| ||||| || || |||||||| ||||| |||||||
---------------------------------------------------gtttttgccatcatagt----ttatgcatttatggatgtctccaatatatgattttaca---gtgcctgctcaatta-gtcag-----gagtttacttt---cctttattttgcagGAACATTTATTAATTGTATGCGAACTTCTCAAGGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCCGGAGGGGAGGTTTACTTCACAATGCCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgagcctacatcatgatgccattgactgtgattaattggaatctcagttttgcagGAGCACCTGTTAATAGTATGTGAACTTCTCAAGGCAAACTTGTATGAGTTCCAAAAGTTTAATAGGGAATCAGGGGGAGAGGTTTATTTCACTATGCCAA
gattaat putative branch site (score: 3)
tgattaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtagatagatgcagaattgtatctttttcttttcaacaccgggtggatattctgctgctttggtgctatgatgtatcaattgttcgattcagtaaagaacatgggacgtgagcctacatcatgatgccattgactgtgattaattggaatctcagttttgcagGAGCACCTGTTAATAGTATGTGAACTTCTCAAGGCAAACTTGTATGAGTTCCAAAAGTTTAATAGGGAATCAGGGGGAGAGGTTTATTTCACTATGCCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG