Sequence
atgc intronic sequence ATGC exonic sequencegtttgtcaaaagaagttgttaccacttgctctgttcttacttcttaccatatgctatgttctccattctttgactacgtttactgttatatacttaaagaaacatgtgtagttcactaataattgacaccggttatattcacagGGAATTGGAAATGGATTGCCATTAGGAGCTGTGGTGACTACACCAGAAATCGCAAGTGTTTTAGCTAGCAAGATTCTGTTCAACACTTTTGGTGGGAACC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G39660.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G39660.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G14850.2 (Glycine max), 3'ss of exon 5
gtttgtcaaaagaagttgttaccacttgctctgttcttacttcttaccatatgctatgttctccattctttgactacgtttactgttatatacttaaagaaacatgtgtagttcactaataattgacaccggttatattcacagGGAATTGGAAATGGATTGCCATTAGGAGCTGTGGTGACTACACCAGAAATCGCAAGTGTTTTAGCTAGCAAGATTCTGTTCAACACTTTTGGTGGGAACC
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---------------------------------------ttttctgccatattttattatggaatttattttgtt---ctcactttttaaccttcatatattctgctgctatttcatcatatctcatgttaatt-tgtat-cagGGTATTGGCAATGGTCTGCCATTAGGAGCTGTAGTTACAACTCCAGAAATTGCAAGTGTGTTGGCCCAAAAGATTCAATTTAATACCTTTGGTGGGAACC
upper sequence: AT4G39660.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv07s0031g01330.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------------------------------gtttgtcaaaagaagttgttaccacttgctctgttcttacttcttaccatatgctatgttctccattctttgactacgtttactgttatatacttaaagaaacatgtgtagttcact--aataattgacaccggttatattca-cagGGAATTGGAAATGGATTGCCATTAGGAGCTGTGGTGACTACACCAGAAATCGCAAGTGTTTTAGCTAGCAAGATTCTGTTCAACACTTTTGGTGGGAACC
||| | | || | || | | ||| | | ||| | | ||| | || || | ||||| | || || | ||| || | || | | | | | || | | ||| | ||||| ||||| ||||| || ||||||||||| |||||||| ||||||||||| ||| ||| || ||| || |||| || |||||||| ||||||||||
gtttctctagtcatccttatagtcttttatggtttttacccatcctgggtggcattgatagtaaaattctatattgcat-ttctttcttggtaacttgttttctag-atgcattacaactttcatttcagtttattatttcatgtcttgtaaaatattgctcaaccattccactgaatttcagaaataacatttatcagGGCATTGGCAATGGTTTACCATTAGGAGCAGTGGTGACAACACCAGAAATAGCAGATGTATTGGCTCAGAAAATTCAATTTAACACTTTCGGTGGGAACC
upper sequence: AT4G39660.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S32_198V6.1 (Physcomitrella patens), 3'ss of exon 5
gtttgtcaaaagaagttgttaccacttgctctgttcttacttcttaccatatgctatgttctccattctttgactacgtttactgttatatacttaaagaaacatgtgtagttcactaataattgacaccggttatattcacagGGAATTGGAAATGGATTGCCATTAGGAGCTGTGGTGACTACACCAGAAATCGCAAGTGTTTTAGCTAGCAAGATTCTGTTCAACACTTTTGGTGGGAACC
| ||| || |||||| | | | | | ||| | | || || | | | | ||| || | || || | ||| | ||||||| |||||||| || ||||| ||||||||| |||||| ||||||||||||||||| ||| || | || | | |||||||| | ||| || || |
----------------------------------ttttaatta--accatacaaca-gcatttagtacattg--tgctttggatgct-tgtcaggagtgaatca-gaacagcgcatttcaaatcgttgt--attatatt-gcagGGAATCGGTAATGGGCTGCCATTAGCAGCTGTAGTGACTACACCAGAAATTGCACAAGTGCTTGCACAACGATTGCATTTCAACACATATGGGGGCAATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atacttaaagaaacatgtgtagttcactaataattgacaccggttatattcacagGGAATTGGAAATGGATTGCCATTAGGAGCTGTGGTGACTACACCAGAAATCGCAAGTGTTTTAGCTAGCAAGATTCTGTTCAACACTTTTGGTGGGAACC
actaataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtcaaaagaagttgttaccacttgctctgttcttacttcttaccatatgctatgttctccattctttgactacgtttactgttatatacttaaagaaacatgtgtagttcactaataattgacaccggttatattcacagGGAATTGGAAATGGATTGCCATTAGGAGCTGTGGTGACTACACCAGAAATCGCAAGTGTTTTAGCTAGCAAGATTCTGTTCAACACTTTTGGTGGGAACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG