Sequence
atgc intronic sequence ATGC exonic sequencegtaacatttgtaaacattgtccaagagttttgctgttccatgatactctcaacctctaagagattatgaccactcactgttgaatgtagATTAATAGCCATATGCGAGGACTTGTACGCGGCTAGAGCAGAGGGTGAGCTTGGAGTAGAAGAAGTTCTATACTGGACGCTTGTGAAGATCTATAGATCC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G48060.1 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G48060.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA10G02870.1 (Glycine max), 3'ss of exon 4
--------------------------------------------------------------------------------------------gtaacatttgtaaacattgtccaagagttttgctgttcc-----atgatac-tctcaacctctaagagattatgaccactcactgttgaatgtagATTAATAGCCATATGCGAGGACTTGTACGCGGCTAGAGCAGAGGGTGAGCTTGGAGTAGAAGAAGTTCTATACTGGACGCTTGTGAAGATCTATAGATCC
||||| | | | | |||| | ||| | || ||||||| || | || | | || | | || | |||||||| ||||| || |||||||| | || || |||||||| ||||||||||||||| | ||||| || || |||||||| || |||||||| || | |||
gtactgcagatttattttctgaaaatggcagtaccaatgatatctttttccccattgagaatgtctagccatttaaacgtgaccgatgtcactgaacatgcgatattctactataagattgttggtaaccctatttatgatacgtcccggttacttacatcttgt---ttcatgcttctcg-tgtagATTGATAGCGATCTGCGAGGATATATATGCTGCTAGAGCTGAGGGTGAGCTTGGAATTGAAGAGGTCCTTTACTGGACTCTAGTGAAGATATACCGGTCC
upper sequence: AT2G48060.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA02G16920.1 (Glycine max), 3'ss of exon 3
--------------------------------------------------------------------------------------------gtaacatttgtaaacattgtcc---aagagttttgctgttcc-----atgatac-tctcaacctctaagagattatgaccactcactgttgaatgtagATTAATAGCCATATGCGAGGACTTGTACGCGGCTAGAGCAGAGGGTGAGCTTGGAGTAGAAGAAGTTCTATACTGGACGCTTGTGAAGATCTATAGATCC
||||| || | | | | |||| | ||||| || ||||||| || | || | || | | | | |||||||| ||||| || |||||||| | || || |||||||| ||||||||||||||| | ||||| || || |||||||| || |||||||| || | |||
gtactacagatttattttctgaagatggcagtaccattcatatctttttccccattgagagtgtctggccacttaaacataactgatgtcactgaacatgcgttattctactactataagattgttgctaaccctatttatgatacatcctgattacttattacttcttgtttcatgtttctcg-tgtagATTGATAGCGATCTGCGAGGATATATATGCTGCTAGAGCTGAGGGTGAGCTTGGAATCGAAGAGGTCCTTTACTGGACTCTAGTGAAGATATACCGGTCC
upper sequence: AT2G48060.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv07s0104g00760.t01 (Vitis vinifera), 3'ss of exon 20
-----------gtaacatttg---taaacattgtccaagagttttgctgttccatgatactctcaacctctaagagattatgaccactcactgttga--atgtagATTAATAGCCATATGCGAGGACTTGTACGCGGCTAGAGCAGAGGGTGAGCTTGGAGTAGAAGAAGTTCTATACTGGACGCTTGTGAAGATCTATAGATCC
|| |||| ||||| | || | | || ||| || || | || | | || | ||| | | | |||||| || |||||||| || ||||| | || || || || ||||||||||||||||||| || || |||| |||||||| || ||||||||||| || ||
cttgctttatcgttgcattcaaactaaacccacttcataaatattcaagtt-----atgcttgagataactgataactttccccaacttgttcattacgatgtagGTTGATAGCCATCTGTGAGGATATATATGCTGCAAGGTCAGAGGGTGAGCTTGGAGTGGAGGAGATTCTCTACTGGACTCTGGTGAAGATCTACAGGTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttccatgatactctcaacctctaagagattatgaccactcactgttgaatgtagATTAATAGCCATATGCGAGGACTTGTACGCGGCTAGAGCAGAGGGTGAGCTTGGAGTAGAAGAAGTTCTATACTGGACGCTTGTGAAGATCTATAGATCC
cactcac putative branch site (score: 2)
agattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacatttgtaaacattgtccaagagttttgctgttccatgatactctcaacctctaagagattatgaccactcactgttgaatgtagATTAATAGCCATATGCGAGGACTTGTACGCGGCTAGAGCAGAGGGTGAGCTTGGAGTAGAAGAAGTTCTATACTGGACGCTTGTGAAGATCTATAGATCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA