Sequence
atgc intronic sequence ATGC exonic sequencegttcgttgtcttcttctgaaaactttggctccattgcaactaattttcttacagtactttgatgaacttctaatttttcagGGTTTAGCATTCCAATTAATAGACGACATTCTTGATTTCACGGGCACATCTGCCTCTCTCGGAAAGGGATCGTTGTCAGATATTCGCCATGGAGTCATAA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G34630.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G34630.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G014508_T03 (Zea mays), 3'ss of exon 9
--------------------gttcgttgtcttcttctgaaaactttggctccattgcaactaatttt---cttacagtactttgatgaacttctaatttttcagGGTTTAGCATTCCAATTAATAGACGACATTCTTGATTTCACGGGCACATCTGCCTCTCTCGGAAAGGGATCGTTGTCAGATATTCGCCATGGAGTCATAA
| | | ||| | |||| | || || || | | | || | | || | || || | |||||| |||| ||||| ||||| || || ||||||||||||| ||||| ||||| || || || ||||| || ||||| |||||||||||
gtttgtaaaacatcttacatttcccgttccttttcttgaattcattaacttgcaagctatttctgttaacttggtgacatcttagttaatttggtgcatg-cagGGTCTAGCCTTCCAGTTAATTGATGATGTTCTTGATTTCACCGGCACCTCTGCATCCCTTGGGAAGGGTTCATTGTCTGATATTCGCCAC----------
upper sequence: AT2G34630.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA17G18160.2 (Glycine max), 3'ss of exon 9
---------------------gttcgttgtcttcttctgaaaactttggctccattgcaactaattttcttacagtactttgatgaacttctaatttttcagGGTTTAGCATTCCAATTAATAGACGACATTCTTGATTTCACGGGCACATCTGCCTCTCTCGGAAAGGGATCGTTGTCAGATATTCGCCATGGAGTCATAA
|| ||||| || | | || | || | ||||| ||| | | || |||| |||||||| ||||| ||||| ||||| || ||||||||||||| |||||||| || || || |||||||| || || ||||| ||||| |||
acaacatatagttaatatctattttcctgtctgtacatgctatatatgtttttgttt--atgaatttccttgaaatttatttccctctccactgttttgcagGGTTTGGCATTTCAATTGATAGATGATGTTCTTGATTTCACAGGCACATCAGCTTCCCTTGGAAAGGGTTCTTTATCAGACATTCGTCAT----------
upper sequence: AT2G34630.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA05G21570.1 (Glycine max), 3'ss of exon 9
----------------gttcgttgtct-----tcttctgaaaactttggctccattgcaactaattttcttacagtactttgatgaacttctaatttttcagGGTTTAGCATTCCAATTAATAGACGACATTCTTGATTTCACGGGCACATCTGCCTCTCTCGGAAAGGGATCGTTGTCAGATATTCGCCATGGAGTCATAA
|| ||||| | || || | | | || || || | ||||| ||| | | || |||| |||||||| ||||| ||||| ||||| || | ||||||||||| |||||||| || || || |||||||| || || ||||| ||||| |||
atatagttaatatctattttcctgtctgtacatgttatgtacagtatgtttctgttt--atgaatttccttgaaatttatttccctctccactgttttgcagGGTTTGGCATTTCAATTGATAGATGATGTGCTTGATTTCACAGGCACATCAGCTTCCCTTGGAAAGGGTTCTTTATCAGACATTCGTCAT----------
upper sequence: AT2G34630.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv06s0009g03090.t01 (Vitis vinifera), 3'ss of exon 1
----------------gttcgttgtcttcttctgaaaactttggctccattgcaactaattttcttacagtactttgatgaacttctaattttt---cagGGTTTAGCATTCCAATTAATAGACGACATTCTTGATTTCACGGGCACATCTGCCTCTCTCGGAAAGGGATCGTTGTCAGATATTCGCCATGGAGTCATAA
||| | | || || || || || || | | | | || || || ||| | ||||| || ||||||||||||||||| ||| | ||||||||||| |||||||| || || || || ||||| || ||||| || || ||| ||
tgatttattgtggagaagatattggtgttgtttgttgtggttttctttcttatgtctctttcaatctgattggtctggtgctgcccttttttctggacagGGATTGGCATTCCAATTAATAGATGACGTCCTTGATTTCACAGGCACATCAGCTTCCCTGGGGAAGGGTTCATTGTCTGACATCCGCAAT----------
upper sequence: AT2G34630.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv00s0283g00050.t01 (Vitis vinifera), 3'ss of exon 1
----------------gttcgttgtcttcttctgaaaactttggctccattgcaactaattttcttacagtactttgatgaacttctaattttt---cagGGTTTAGCATTCCAATTAATAGACGACATTCTTGATTTCACGGGCACATCTGCCTCTCTCGGAAAGGGATCGTTGTCAGATATTCGCCATGGAGTCATAA
||| | | || || || || || || | | | | || || | ||| | ||||| || ||||||||||||||||| ||| | ||||||||||| |||||||| || || || || ||||| || ||||| || || ||| ||
tgatttattgtggagaagatattggtgttgtttgctgtggttttctttcttatgtctctttcaatctgattggtctggtgctgcctttttttctggacagGGATTGGCATTCCAATTAATAGATGACGTCCTTGATTTCACAGGCACATCAGCTTCCCTGGGGAAGGGTTCATTGTCTGACATCCGCAAT----------
upper sequence: AT2G34630.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv15s0024g00850.t01 (Vitis vinifera), 3'ss of exon 9
----------------gttcgttgtcttcttctgaaaactttggctccattgcaactaattttcttacagtactttgatgaacttctaattttt---cagGGTTTAGCATTCCAATTAATAGACGACATTCTTGATTTCACGGGCACATCTGCCTCTCTCGGAAAGGGATCGTTGTCAGATATTCGCCATGGAGTCATAA
||| | | || || || || || || | | | | || || || ||| | ||||| || ||||||||||||||||| ||| | ||||||||||| |||||||| || || || || ||||| || ||||| || || ||||||
tgatttattgtggagaagatattggtgttgtttgctgtggttttctttcttatgtctctttcaatctgattggtctggtgctgcccttttttctggacagGGATTGGCATTCCAATTAATAGATGACGTCCTTGATTTCACAGGCACATCAGCTTCCCTGGGGAAGGGTTCATTGTCTGACATCCGCCAT----------
upper sequence: AT2G34630.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv03s0132g00010.t01 (Vitis vinifera), 3'ss of exon 1
----------------gttcgttgtcttcttctgaaaactttggctccattgcaactaattttcttacagtactttgatgaacttctaattttt---cagGGTTTAGCATTCCAATTAATAGACGACATTCTTGATTTCACGGGCACATCTGCCTCTCTCGGAAAGGGATCGTTGTCAGATATTCGCCATGGAGTCATAA
||| | | || || || || || || | | | | || || || ||| | ||||| || ||||||||||||||||| || | ||||||||||| |||||||| || || || || ||||| || ||||| || || || ||
tgatttattgtggagaagatattggtgttgtttgctgtggttttctttcttatgtctctttcaatctgattggtctggtgctgcccttttttctggacagGGATTGGCATTCCAATTAATAGATAACGTCCTTGATTTCACAGGCACATCAGCTTCCCTGGGGAAGGGTTCATTGTCTGACATCCGTAAT---------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggctccattgcaactaattttcttacagtactttgatgaacttctaatttttcagGGTTTAGCATTCCAATTAATAGACGACATTCTTGATTTCACGGGCACATCTGCCTCTCTCGGAAAGGGATCGTTGTCAGATATTCGCCATGGAGTCATAA
ttctaat putative branch site (score: 2)
tttttc CT-rich tract
aactaattttctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcgttgtcttcttctgaaaactttggctccattgcaactaattttcttacagtactttgatgaacttctaatttttcagGGTTTAGCATTCCAATTAATAGACGACATTCTTGATTTCACGGGCACATCTGCCTCTCTCGGAAAGGGATCGTTGTCAGATATTCGCCATGGAGTCATAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA