Sequence
atgc intronic sequence ATGC exonic sequencegtaagttccttttcttctgtttcctctctattccttgacaaaagatggagaaatgagcaccaatgttacctaaatctgtggcagGCGAGTTATCGAGGGGCGATACTTTTGTTGATGGAGCAGTTATCGCTGCAGCAAGAACATTACCTACTTGGTCAGACATAGATCTTCCTCCAATACCGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G20130.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G20130.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA15G16830.1 (Glycine max), 3'ss of exon 10
-----------gtaagttccttttcttctgtttcctctctatt--ccttgacaaaagatggagaaatgagcaccaatgttacct--aaatctgtggcagGCGAGTTATCGAGGGGCG---ATACTTTTGTTGATGGAGCAGTTATCGCTGCAGCAAGAACATTACCTACTTGGTCAGACATAGATCTTCCTCCAATACCGAG
| | || ||||| | | || | | ||| | | | | || | || | | |||| | |||||| | || | | || ||| |||||||||||||||||| || ||||||||| ||||||| || ||||||||||| ||| | |||||||| ||
gtatgggcaatatgaattttctttctggaatcttctatgttacagttttgtctattcaaattggcattatttaggatatcaatatgaaatttatggcagATTGTCTGTCAAAAGCCGGAGATAGTTTTGTTGATGGAGCAGTCATAGCTGCAGCACGAACATTGCCAACTTGGTCAGATGGGGATGTGCCTCCAATCCC---
upper sequence: AT4G20130.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA09G05510.1 (Glycine max), 3'ss of exon 10
-----------gtaagttccttttcttctgtttcctctctattccttgacaa---aagatggagaaatgagcaccaatgttacctaaatctgtggcagGCGAGTTATCGAG---GGGCGATACTTTTGTTGATGGAGCAGTTATCGCTGCAGCAAGAACATTACCTACTTGGTCAGACATAGATCTTCCTCCAATACCGAG
| | || ||||| | | || | ||| | | || ||| || | | || |||| | |||||| | || | || |||| |||||||||||||||||| || ||||||||| ||||| | || | ||||||||| ||| | |||||||| ||
gtatgggcaatatgaattttctttctggaatctgctgttacagttttgtctattcaaattggcattatttaggatatcgatatg-aaatttatggcagATTGTCTGTCAAATGCTGGGGATAGTTTTGTTGATGGAGCAGTCATAGCTGCAGCACGAACACTGCCAAGTTGGTCAGATGGGGATGTGCCTCCAATCCC---
upper sequence: AT4G20130.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv01s0011g01080.t01 (Vitis vinifera), 3'ss of exon 10
-------------------------gtaagttccttttcttctgtttcctctctattccttgacaaaagatggagaaatgag-cacc-aatgttacctaaatctgtggcagGCGAGTTATCGAGG---GGCGATACTTTTGTTGATGGAGCAGTTATCGCTGCAGCAAGAACATTACCTACTTGGTCAGACATAGATCTTCCTCCAATACCGAG
||| | | || | | | | || | | | | || | | | | || ||| | || | ||| ||||| |||||| | || |||| ||||||||||||||| || || || |||||||||||||| || ||||||||||| ||| | |||||||| ||
gtatgggtcaatgaatcttctcttcataaatgcagtt-catatatatcacattttcttgtaattaagccctagcatttttattcattgaatcccataaaattttgtagcagGTCGGTTATCTAATAATGGAGATAGTTTTGTTGATGGAGCGGTAATAGCAGCAGCAAGAACATTGCCCACTTGGTCAGATGGGGATGTGCCTCCAATGCC--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attccttgacaaaagatggagaaatgagcaccaatgttacctaaatctgtggcagGCGAGTTATCGAGGGGCGATACTTTTGTTGATGGAGCAGTTATCGCTGCAGCAAGAACATTACCTACTTGGTCAGACATAGATCTTCCTCCAATACCGAG
acctaaa putative branch site (score: 3)
aaaagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttccttttcttctgtttcctctctattccttgacaaaagatggagaaatgagcaccaatgttacctaaatctgtggcagGCGAGTTATCGAGGGGCGATACTTTTGTTGATGGAGCAGTTATCGCTGCAGCAAGAACATTACCTACTTGGTCAGACATAGATCTTCCTCCAATACCGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC