Sequence
atgc intronic sequence ATGC exonic sequencegttagaaactcttaaaaattctaagatttcaatacaaataactgaaagagcttccagagatgaaaaaattactgataaactgtttttctacagATTCTGAAATGCTGAAGGATGTTTCAAGATATACAAGACAAGAGCTAGAAGTAGCATGTGAAGACTTCAGCAACATCATTGATTCTAGTGCAGAGAGTCA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G41180.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G41180.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA11G02690.1 (Glycine max), 3'ss of exon 8
---gttagaaactcttaaaaattctaagatttcaatacaaataactgaaagagcttccagagatgaaaaaattactgataaactgtttt--tctacagATTCTGAAATGCTGAAGGATGTTTCAAGATATACAAGACAAGAGCTAGAAGTAGCATGTGAAGACTTCAGCAACATCATTGATTCTAGTGCAGAGAGTCA
|||| || || ||| |||| || | || || || ||| |||| || | | | || || | || | | |||| |||| || |||| ||||| ||| |||| ||||||||||| ||||| || |||||||||||||||||||| |||| || |||| |||
gtatgtagattctgtttctttttccctactttctatttacat--ct---agtatttctagagctgttttcaaca-taattggctttattaatgtgcagACCCTGAGTTGTTGAAAGATGTGAGAAGGTATAGCAGACAAGAGCTTGAAGTTGCCTGTGAAGACTTCAGCAACATAATTGGGTCCTCACCAGATAGTGT
upper sequence: AT5G41180.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA01G42770.1 (Glycine max), 3'ss of exon 9
gttagaaactcttaaaaattctaagatttcaatacaaataactgaaagagcttccagagatgaaaaaattactgataaactgtttt--tctacagATTCTGAAATGCTGAAGGATGTTTCAAGATATACAAGACAAGAGCTAGAAGTAGCATGTGAAGACTTCAGCAACATCATTGATTCTAGTGCAGAGAGTCA
|| | | | | || | | | || | ||| |||| || | | | || || | || | | |||| |||| | |||||||||| ||| |||| ||||| ||||| ||||| || |||||||||||||||||||| |||| || |||| |||
gtatgtagattctgtt--tttttgccccctactttctatttacattaatatttctagagctgttttcaaca-taattggctttattaatgtgcagACCCTGAGTTTTTGAAGGATGTGAGAAGGTATAGCAGACAGGAGCTTGAAGTTGCCTGTGAAGACTTCAGCAACATAATTGGGTCCTCACCAGATAGTGT
upper sequence: AT5G41180.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv02s0025g03700.t01 (Vitis vinifera), 3'ss of exon 8
----gttagaaactcttaaaaattctaagatttcaatacaaataactgaaagagcttcc--agagatgaaaaaattactgataaactgtttttctacagATTCTGAAATGCTGAAGGATGTTTCAAGATATACAAGACAAGAGCTAGAAGTAGCATGTGAAGACTTCAGCAACATCATTGATTCTAGTGCAGAGAGTCA
| | |||| | | || || | | || | |||| ||| || ||| | | | | | || || ||||| ||||| ||| |||||||||| | |||| | || |||||||| ||||||||||||||||| ||||||||||| || | || |||| |||
gtaaaattgttactcaacagtccgccccatttgcactttatatctcagaaaccttttctttagtattgatggcagtgttctttcattgatt----acagACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAGTAGCATGTGAAGATTTCAGCAACATAATAGGCTCCTCACCAGATAGTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taactgaaagagcttccagagatgaaaaaattactgataaactgtttttctacagATTCTGAAATGCTGAAGGATGTTTCAAGATATACAAGACAAGAGCTAGAAGTAGCATGTGAAGACTTCAGCAACATCATTGATTCTAGTGCAGAGAGTCA
tactgat putative branch site (score: 2)
ctgtttttct putative PPT
aaaaaattactgataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagaaactcttaaaaattctaagatttcaatacaaataactgaaagagcttccagagatgaaaaaattactgataaactgtttttctacagATTCTGAAATGCTGAAGGATGTTTCAAGATATACAAGACAAGAGCTAGAAGTAGCATGTGAAGACTTCAGCAACATCATTGATTCTAGTGCAGAGAGTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA