Sequence
atgc intronic sequence ATGC exonic sequencegttagttcttttttgtgtacattacaaacagagccatgaggttcaaccctgaacaggtttaggagtcatgcttaatattttctttcccctcattttaaggactctaatatggtctttttcagGTTGATAGGCTACTTTCATCTGAGCAGAAGTCTACTGATTATAGATCAACTGATGATGGAATTGCTTCTGACCACCGTCCAACAAATGCCTGCATAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G12370.1 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G12370.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA16G01660.1 (Glycine max), 3'ss of exon 18
gttagttcttttttgtgtacattacaaacagagccatgaggttcaaccctgaacaggtttaggagtcatgcttaatattttctttcccctcattttaaggactctaatatggtcttttt--cagGTTGATAGGCTACTTTCATCTGAGCAGAAGTCTACTGATTATAGATCAACTGATGATGGAATTGCTTCTGACCACCGTCCAACAAATGCCTGCATAAG
||||| || | || | | || || | ||| ||| | || | || | |||| | |||| | || | | | | || ||||| || || | |||||| |||| || ||| |||| |||||| ||||| ||||||||||||| ||| |||||||||| |||| | |||||||| |||
---------tttttctgg----ttcagggtgtttcctgtattttttct---------ttttcttttcaagtttga-atcctagctcccaaactcttaaa-attccactttaaaccccttggcagGTGGAGCGGTTGCTTTCAGCTGAACAAAAGGCTACAGATTATCGATCACCTGATGATGGAATGGCTCCTGACCACCGGGCAACCAGTGCCTGCACAAG
upper sequence: AT5G12370.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA07G05160.1 (Glycine max), 3'ss of exon 18
gttagttcttttttgtgtacattacaaacagagccatgaggttcaaccctgaacaggtttaggagtcatgcttaatattttctttcccctcattttaaggactctaatatggtcttttt--cagGTTGATAGGCTACTTTCATCTGAGCAGAAGTCTACTGATTATAGATCAACTGATGATGGAATTGCTTCTGACCACCGTCCAACAAATGCCTGCATAAG
|| | | || | | || | || | ||| | ||| | || | | | |||| | |||| | || | | | | || ||||| || || | |||||| |||| || ||| |||| |||||| ||||| ||||||||||||| ||| |||||||||| |||| | |||||||| |||
--------------gtttctggttcagggtgtttcctgtgttttttct---------ttttctaatcaagtttga-accctagctcccaaactcttaaatattccactttaaaccccttggcagGTGGAGCGGTTGCTTTCAGCTGAACAAAAGGCTACAGATTATCGATCACCTGATGATGGAATGGCTCCTGACCACCGGGCAACCAGTGCCTGCACAAG
upper sequence: AT5G12370.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: Vv15s0046g02200.t01 (Vitis vinifera), 3'ss of exon 18
gttagttcttttttgtgtacattacaaacagagccatgaggttcaaccctgaacaggtttaggagtcatgcttaatattttctttcccctcattttaaggactctaatatggtctttttcagGTTGATAGGCTACTTTCATCTGAGCAGAAGTCTACTGATTATAGATCAACTGATGATGGAATTGCTTCTGACCACCGTCCAACAAATGCCTGCATAAG
| | | || || | | || ||| || || | | ||| | ||| |||| || || | | | | ||| | |||| | ||||| || || |||| ||| |||| |||||| | || |||||| | | ||||||||||||||||| |||| || || |||||||||||||||| ||
gcttgaatcttcttctactcttt-----cagcatcacttatttggtgctcttatgattttcattcttatg-ttaagatattttgttct--------------tgtaaaac--tcttgtgcagGTGGAGCGGTTACTATCAGCTGAACAGAAGGCAACAGATTATCGGTTGCCTGATGATGGAATTGCTCCTGATCATCGGCCAACAAATGCCTGCACTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgcttaatattttctttcccctcattttaaggactctaatatggtctttttcagGTTGATAGGCTACTTTCATCTGAGCAGAAGTCTACTGATTATAGATCAACTGATGATGGAATTGCTTCTGACCACCGTCCAACAAATGCCTGCATAAG
ctctaat putative branch site (score: 3)
tctttttc putative PPT
taatattttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagttcttttttgtgtacattacaaacagagccatgaggttcaaccctgaacaggtttaggagtcatgcttaatattttctttcccctcattttaaggactctaatatggtctttttcagGTTGATAGGCTACTTTCATCTGAGCAGAAGTCTACTGATTATAGATCAACTGATGATGGAATTGCTTCTGACCACCGTCCAACAAATGCCTGCATAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA