Sequence
atgc intronic sequence ATGC exonic sequence...gaatgagaaaatataccaaaacatttggtatggattcaaaatatggatcattgttgcaagttgtaactaaaccatgtccatgcctactattttcctgcagGTTGGAGCAATTATCTCTGGTATTCAGCCTGGGCTAACTATGGTGGTTGGTCCACCAGGTACCGGAAAGACTGATACAGCAGTGCAAATTTTGAATGTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G38770.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G38770.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os03g26960.1 (Oryza sativa), 3'ss of exon 11
gaatgagaaaatataccaaaacatttggtatggattcaaaatatggatcattgttgcaagt--tgtaacta-aaccatgtccatgcctactatttt--cctgcagGTTGGAGCAATTATCTCTGGTATTCAGCCTGGGCTAACTATGGTGGTTGGTCCACCAGGTACCGGAAAGACTGATACAGCAGTGCAAATTTTGAATGTTC
| | ||| ||||| || | | ||| | | | | | || | ||||| | | ||| | | | ||| | || || |||| || || || ||||||||||| |||||| | || ||||| |||||||| || ||||| ||||| || |||||||| ||||| || |||||||||
----ttattattttacttgcttatttga-atttgcttgagatacacaaccatatgacttgtcctttaactttagctctgttggtaacaatctcttttacttgtagATTGGTGCTATAATATCTGGTATTCAACCTGGGTTGACAATGGTTGTTGGTCCTCCTGGTACGGGAAAAACAGATACAGCTGTGCAGATATTGAATGTTT
upper sequence: AT2G38770.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G410479_T01 (Zea mays), 3'ss of exon 12
gaatgagaa-aatataccaaaacatttggtatggattcaaaatatggatcattgttgcaagttgtaactaaaccatgtccatgcc--tactattttcctgcagGTTGGAGCAATTATCTCTGGTATTCAGCCTGGGCTAACTATGGTGGTTGGTCCACCAGGTACCGGAAAGACTGATACAGCAGTGCAAATTTTGAATGTTC
|||| || | ||| | | | || |||| || | | | || ||| || || | || | || ||||| || || | || || || || ||||||||||| |||||| | || ||||| |||||||| || ||||| ||||| || ||||| || ||||| || || |||||||
gaataagtctagtatggtctgctagtgtctttgctttcatgatgagtgtggatcttattcaccttaa---aattctgactgtgacaatattatttatttgtagATCGGTGCTATAATATCTGGTATTCAACCTGGGTTGACGATGGTTGTTGGTCCTCCTGGTACGGGAAAAACAGATACTGCTGTGCAGATATTAAATGTTC
upper sequence: AT2G38770.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA20G00260.1 (Glycine max), 3'ss of exon 10
gaatgagaaaatataccaaaacatttggtatggattcaaaatatggatc-attgttgcaagttgtaactaaaccatgtccatgcctactattttcctgcagGTTGGAGCAATTATCTCTGGTATTCAGCCTGGGCTAACTATGGTGGTTGGTCCACCAGGTACCGGAAAGACTGATACAGCAGTGCAAATTTTGAATGTTC
| || | | || ||| | | | ||| || | | | | | || || | | || || |||||||| |||||| |||||||| ||||||||||| ||||||||||| || || ||||| ||||| ||||||||||||||||| || |||||| | |||||||
-tccccacatgtactttatgtctttatcctcttatttatattccctatctatgagtattggataaatattaataatagtgtgaaatgttcttatcaagcagGTTGAAGCAATCATCTCTGGCATTCAGCCTGGTCTAACTATGGTTGTGGGGCCACCTGGTACAGGAAAGACTGATACAGCTGTACAAATTCTAAATGTTC
upper sequence: AT2G38770.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA0048S00340.1 (Glycine max), 3'ss of exon 10
gaatgagaaaatataccaaaacatttggtatggattcaaaatatggatcat-tgttgcaagttgtaactaaaccatgtccatgcctactattttcctgcagGTTGGAGCAATTATCTCTGGTATTCAGCCTGGGCTAACTATGGTGGTTGGTCCACCAGGTACCGGAAAGACTGATACAGCAGTGCAAATTTTGAATGTTC
| | | || | | || ||| | | |||| ||| || | | | | | || || | | | || |||||||| |||||| |||||||| ||||||||||| ||||||||||| || || ||||| ||||| ||||||||||||||||| || |||||| | |||||||
-cccatatatacttccccacatgttctttatcctcttattatattccccatctgatatttgattaatattaataatagtgtgaaatgttcctatcaagcagGTTGAAGCAATCATCTCTGGCATTCAGCCTGGTCTAACTATGGTTGTGGGGCCACCTGGTACAGGAAAGACTGATACAGCTGTACAAATTCTAAATGTTC
upper sequence: AT2G38770.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv08s0056g01110.t01 (Vitis vinifera), 3'ss of exon 10
gaatgagaaaatataccaaaacatttggtatggattcaaaatatggatcattgttgcaagttgtaactaaaccatgtccatgcctactattttcctgcagGTTGGAGCAATTATCTCTGGTATTCAGCCTGGGCTAACTATGGTGGTTGGTCCACCAGGTACCGGAAAGACTGATACAGCAGTGCAAATTTTGAATGTTC
||| | | | | |||| ||| ||||| | || | ||| | | || || | | | | | ||||| ||| |||||| | || ||||||||||| || |||| ||||| || |||||||| ||||| ||||||||||| || || ||||| || ||||||||||
ttatggattgtgaaagttacatttttgaatgggagggaaaatgttcattgctattgactttgtcttttttactatttaccttaatgtgtctgctatgcagATTGTAGCAATCAATTCAGGTATTCAGCCAGGCTTAACAATGGTTGTGGGTCCACCTGGTACAGGAAAGACTGACACTGCTGTGCAGATCTTGAATGTTC
upper sequence: AT2G38770.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv13s0019g00880.t01 (Vitis vinifera), 3'ss of exon 10
-----gaatgagaaaatataccaaaacatttggtatggattcaaaatatggatcattgttgcaagttgtaactaaaccatgtccatgcctactattttcctgcagGTTGGAGCAATTATCTCTGGTATTCAGCCTGGGCTAACTATGGTGGTTGGTCCACCAGGTACCGGAAAGACTGATACAGCAGTGCAAATTTTGAATGTTC
|| || |||| | | | ||| | ||| ||||| | || | ||| | | || || | | | | | ||||| |||||||||| | || ||||||||||| || |||| ||||| || |||||||| ||||| ||||||||||| || || ||||| || ||||||||||
ttatagattgtgaaag----ctacattttttaatg-ggagggaaaatgttcattgctattgactctgtctttttgactatttaccttaatgtctctgctatgcagATTGGAGCAATCAGTTCAGGTATTCAGCCAGGCTTAACAATGGTTGTGGGTCCACCTGGTACAGGAAAGACTGACACTGCTGTGCAGATCTTGAATGTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatcattgttgcaagttgtaactaaaccatgtccatgcctactattttcctgcagGTTGGAGCAATTATCTCTGGTATTCAGCCTGGGCTAACTATGGTGGTTGGTCCACCAGGTACCGGAAAGACTGATACAGCAGTGCAAATTTTGAATGTTC
aactaaa putative branch site (score: 2)
cctactattttcct putative PPT
tactatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaatgagaaaatataccaaaacatttggtatggattcaaaatatggatcattgttgcaagttgtaactaaaccatgtccatgcctactattttcctgcagGTTGGAGCAATTATCTCTGGTATTCAGCCTGGGCTAACTATGGTGGTTGGTCCACCAGGTACCGGAAAGACTGATACAGCAGTGCAAATTTTGAATGTTC
- - - gaaaata
- - - - - - - -ccaaaac
- - - - - - - - - - - - - ggtatgg
- - - - - - - - - - - - - - - - - - caaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatgcc