Sequence
atgc intronic sequence ATGC exonic sequencegttcacttcattgctaaacaaaaagcctacagttctgtttaaattgattaacccatccattatttttttcacagGCTGGTGAACTTATAGCCAATCTTGATCTTGATGATCCTTCTGCTGTAAGAAAGGCCGAACCCTTCCATGGAAGTTTCCCAAGATTAGGGCTTCCAACTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G36160.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G36160.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: LOC_Os05g22940.1 (Oryza sativa), 3'ss of exon 21
--------gttcacttcattgctaaacaaaaagcctacagttctgtttaaattgattaacccatccattattt-ttttcacagGCTGGTGAACTTATAGCCAATCTTGATCTTGATGATCCTTCTGCTGTAAGAAAGGCCGAACCCTTCCATGGAAGTTTCCCAAGATTAGGGCTTCCAACTG
| || | |||| | || ||| ||| || | | || || | || ||| || | |||||||||| |||||||| | || ||||||||||| ||||||||||| | | || || || ||| | | | ||| ||| | | || || || | ||
gtacattcctacattccattcattg-tgctgtgctgacatgaacatttcaagtaaata-cctgtaacttgtttattattctagGCTGGTGATCTTATAGCTAGGCTGGATCTTGATGACCCTTCTGCTGTTAAGAGAGCTGAGCCGTTCGAAGATACTTTTCCACAAATGGGTCTCCCTATTG
upper sequence: AT1G36160.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: AC197672.3_FGT002 (Zea mays), 3'ss of exon 19
-------------------gttcacttcattgctaaacaaaaagcctacagttctgtttaaattgattaacccatccattatttttttcacagGCTGGTGAACTTATAGCCAATCTTGATCTTGATGATCCTTCTGCTGTAAGAAAGGCCGAACCCTTCCATGGAAGTTTCCCAAGATTAGGGCTTCCAACTG
||| | ||||| | | | || || | |||| ||| ||| | || ||| ||| | ||||||||| |||||||| | || ||||||||||| ||||||||||| | || || ||||| || |||||| || ||| | | | || || ||
gttatattcatacatgtccattccttgcattgttgctttcatcacatagtatttcatgtaaa---atttaccaacttatattttgtttta--gGCTGGTGATCTTATAGCAAGGCTGGATCTTGATGACCCTTCTGCTGTGAAAAGAGCTGAACCATTTGATGGAATGTTTCCACTAATGGACCTCCCTGTTG
upper sequence: AT1G36160.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 18
-----gttcacttcattgctaaacaaaaagcctacagttctgtttaaattgattaacccatccattatttttttcacagGCTGGTGAACTTATAGCCAATCTTGATCTTGATGATCCTTCTGCTGTAAGAAAGGCCGAACCCTTCCATGGAAGTTTCCCAAGATTAGGGCTTCCAACTG
|| | ||| | | || | |||| || || ||| | | | || |||||||||||||||||||| | |||||||| ||||||||||| |||||||||||||| ||||||||| ||| || |||||| | || | ||| ||||
gtatatagcattctattccacattggaagtacaggtgttcatattgaaagagataataaaatagtatcactgtttgcagGCTGGTGAACTTATAGCAAGGCTTGATCTGGATGATCCTTCAGCTGTAAGAAAGGCAGAACCCTTCACTGGGAGCTTCCCAGTTCTGGGACCTCCTACTG
upper sequence: AT1G36160.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 18
-----gttcacttcattgctaaacaaaaagc-ctacagttctgtttaaattgattaacccatccattatttttttcacagGCTGGTGAACTTATAGCCAATCTTGATCTTGATGATCCTTCTGCTGTAAGAAAGGCCGAACCCTTCCATGGAAGTTTCCCAAGATTAGGGCTTCCAACTG
|| | ||| | | | | ||| | | ||| || || ||| | | ||| |||||||||||||||||||| | |||||||| ||||||||||| |||||||||||||| ||||||||| ||| || |||||| | || | ||| || |
gtatatagcattctatt-ccacataggaagtacaattgttgaaattgaaaaagataataaaattgtatcaccttttgcagGCTGGTGAACTTATAGCAAGGCTTGATCTGGATGATCCTTCAGCTGTAAGAAAGGCAGAACCCTTCACTGGGAGCTTCCCAGTCCTGGGACCTCCTACCG
upper sequence: AT1G36160.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 19
gttcacttcattgctaaacaaaaagcctacagttctgtttaaattgattaacccatccattatttttttcacagGCTGGTGAACTTATAGCCAATCTTGATCTTGATGATCCTTCTGCTGTAAGAAAGGCCGAACCCTTCCATGGAAGTTTCCCAAGATTAGGGCTTCCAACTG
|| | | || | | || || | || | | | | || | |||| |||||||||| |||||||| | |||||||| |||||||||||||||||||| || || || || |||||||| || || |||| ||||||| ||| ||||
gtaaaatatgttccatattggaagttttagtatcctatccttggtaga-gattaagaaatcacattttgtgtagGCTGGTGAGCTTATAGCAAGACTTGATCTAGATGATCCTTCTGCTGTAAGGAAAGCAGAGCCTTTCCATGGGAGCTTTCCAATTTTAGGGCCTCCCACTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaaagcctacagttctgtttaaattgattaacccatccattatttttttcacagGCTGGTGAACTTATAGCCAATCTTGATCTTGATGATCCTTCTGCTGTAAGAAAGGCCGAACCCTTCCATGGAAGTTTCCCAAGATTAGGGCTTCCAACTG
gattaac putative branch site (score: 2)
tccattatttttttc putative PPT
tgtttaaattgattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcacttcattgctaaacaaaaagcctacagttctgtttaaattgattaacccatccattatttttttcacagGCTGGTGAACTTATAGCCAATCTTGATCTTGATGATCCTTCTGCTGTAAGAAAGGCCGAACCCTTCCATGGAAGTTTCCCAAGATTAGGGCTTCCAACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG