Sequence
atgc intronic sequence ATGC exonic sequence...agggttaagatagctttgtttgggcatgtgaggcgtttaggtttccggatgggtggtattacagttttgccttggttgtctaatttttttcctttttcagGATAAGATGGTAAGGAAACCGGTCGACCCGGAAGAGGAATTACGGTGGATGTCCCAAGAAGTACGGGGTTATGTTGAAGCTGTTCTCAACAGTCTAGCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G59610.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GRMZM5G870253_T01 (Zea mays), 3'ss of exon 2
agggttaagatagcttt--gtttgggcatgtgaggcgtttag--gtttccggatgggtggtattacagttttgccttggttgtctaatttttttcctttttcagGATAAGATGGTAAGGAAACCGGTCGACCCGGAAGAGGAATTACGGTGGATGTCCCAAGAAGTACGGGGTTATGTTGAAGCTGTTCTCAACAGTCTAGCTG
||| || || | | |||||| | |||| || ||| | | | | ||| ||| || | || | ||||| | ||| |||||| |||| ||| || | || || ||||| ||| | || |||||||| |||||||| || |||||||||||||||||| | |||||| | ||||
--ttttatcttacctaaaggctaaagcatgtttt-catttaaatgtatccaaacacaagatcacttattttactcttcattctacaactcttttc-tgtttaagGATACAATGGCTCGGAGGCCTGCTGATCCTGAAGAAGAACTTCGATGGATGTCTCAAGAAGTCCGTGGTTATGTTGAAGCTGTTTTGAACAGTTTGGCTG
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 18
agggttaagatagctttgtttgggcatgtgag-gcgtttaggtttccggatgggtggtattacagttttgccttggttgtctaattttttt-----------cctttttcagGATAAGATGGTAAGGAAACCGGTCGACCCGGAAGAGGAATTACGGTGGATGTCCCAAGAAGTACGGGGTTATGTTGAAGCTGTTCTCAACAGTCTAGCTG
||||| || | | | | ||| | | | | || ||| | || | ||||| | | || |||||| ||||| |||||||| | || || || ||||| | | |||||||| |||||||| || |||||||||||||||||||| ||||| || || |
------------gcttttttagaaggtacaaacatgaaccaatttacagtccatctagaattcactttcggtttcttatatcaatttctccatgttgcaaaatcattcaaagGATACGATGGCCAGGAAACCTGCAGATCCAGAGGAGGAGCTCAGATGGATGTCTCAAGAAGTCCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTTGCAG
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 18
-----agggttaagatagctttgtttgggcatgtgaggcgtttaggtttccggatggg--tggtattacagttttgccttggttgtctaatttttttcctttttcagGATAAGATGGTAAGGAAACCGGTCGACCCGGAAGAGGAATTACGGTGGATGTCCCAAGAAGTACGGGGTTATGTTGAAGCTGTTCTCAACAGTCTAGCTG
| | | || | | | |||| ||| | || | || ||| ||| || || ||| || | | | |||||| ||||| || ||||| | || || |||||||| | | |||||||| |||||||| || |||||||||||||||||||| ||||| || ||||
cttttttagaaggtacaaacatgaaccaatttacagtccatctaggattcactttcggattctcataacaatttctccatg-ttgcaaaaat------cgtccgtagGATACGATGGCCAGAAAACCTGCAGATCCAGAAGAGGAGCTCAGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTCGCTG
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 18
agggttaagatagctttgtttgggcatgtgaggcgtttaggtttccggatgggtggtattacag-ttttgccttggttgtctaatttttttcc---tttttcagGATAAGATGGTAAGGAAACCGGTCGACCCGGAAGAGGAATTACGGTGGATGTCCCAAGAAGTACGGGGTTATGTTGAAGCTGTTCTCAACAGTCTAGCTG
| | || | | ||| | ||| || || ||||| ||||| | ||| | || || |||| |||||| |||| || | ||| | ||| || ||||| || | || |||||||| |||||||| || |||||||||||||||||||| ||||| || ||||
--ttctgtactggccccagaacataaattctatagttcacattttttcatt--tgttattaggtcttttgtggttactgtttggttgccttgaaaattttatagGATACAATGGCCAGAAGACCTGCCGATCCAGAAGAAGAGCTCCGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTG
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 18
agggttaagatagctttgtttgggcatgtgaggcgtttaggtt-tccggatgggtggtattacagttttgcct-tggttgtctaatttttttcctttttcagGATAAGATGGTAAGGAAACCGGTCGACCCGGAAGAGGAATTACGGTGGATGTCCCAAGAAGTACGGGGTTATGTTGAAGCTGTTCTCAACAGTCTAGCTG
| || | ||| ||| | || || | | | | ||||| ||| | || |||| | | | ||||||||||| ||||| | | ||| | |||||| ||||| ||| | || |||||||| |||||||| || || ||||||||||| ||| | |||||||| ||||
--cctattgacatttttttttaaaattatgccttaaataagcaatttagttcccctatattatggttccttgtatgattgttgatctgaaattgcttttcagGATACAATGGTCCGAAGACCTGCCGACCCAGAAGAAGAACTTCGATGGATGTCTCAAGAAGTGCGTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cggatgggtggtattacagttttgccttggttgtctaatttttttcctttttcagGATAAGATGGTAAGGAAACCGGTCGACCCGGAAGAGGAATTACGGTGGATGTCCCAAGAAGTACGGGGTTATGTTGAAGCTGTTCTCAACAGTCTAGCTG
gtctaat putative branch site (score: 3)
ttgtctaatttttttc CT-rich tract
taatttttttcctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agggttaagatagctttgtttgggcatgtgaggcgtttaggtttccggatgggtggtattacagttttgccttggttgtctaatttttttcctttttcagGATAAGATGGTAAGGAAACCGGTCGACCCGGAAGAGGAATTACGGTGGATGTCCCAAGAAGTACGGGGTTATGTTGAAGCTGTTCTCAACAGTCTAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - tgtttgg