Sequence
atgc intronic sequence ATGC exonic sequencegtacatctaatggtcatagtattgtctgtcgtacagagtaatatcaccacacagatgtttttttcggagtctgattttttctcttattaatagGCGGCTTATAATTCCGCTAAGTCAAAGAACAAGTTCCATCTTTGGGGTAGCCATTGGAGACATGGAGATTCGTTACTTTTTTCTCTTGCATGTGCTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G51150.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G51150.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os07g31260.1 (Oryza sativa), 3'ss of exon 3
gtacatctaatggtcatagtattgtctgtcgtacagagtaatatcaccacacagatgtttttttcggagtctgattttttctcttattaatagGCGGCTTATAATTCCGCTAAGTCAAAGAACAAGTTCCATCTTTGGGGTAGCCATTGGAGACATGGAGATTCGTTACTTTTTTCTCTTGCATGTGCTCAG
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--gtcaccaactgctaaactgttgcattttatatggtg-aagatgcatgtatggcccttttcctcatgtattgatgcttggtttttacagTGTGCA---TATAATTCTGCAAAGTCTAAGAACAGATTTCACTTTTGGGGAAGCCATTGGAGGCATGGAGATGCATTACTTTTTTCACTTGCGTCTGCCCAG
upper sequence: AT5G51150.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G175799_T02 (Zea mays), 3'ss of exon 3
gtacatctaatggtcatagtattgtctgtcgtacagagta---atatcaccacacaga---tgtttttttcggagtctgattttttctcttattaata----gGCG-GCTTATAATTCCGCTAAGTCAAAGAACAAGTTCCATCTTTGGGGTAGCCATTGGAGACATGGAGATTCGTTACTTTTTTCTCTTGCATGTGCTCAG
||| | | | || | | ||| | ||| || | | | || | | ||| | || | || |||||| | | || |||||||| || || || |||||||| || ||| ||||||| ||||||||||||||||||||| | || |||||||| | |||||||| |||
--gtcattaacagctaaacagtttgttcatatggagaaaatggatagaactatagaagaccaattatacatgaagtattgattcattactgcttaatattgcagTGTGCATATAATTCTGCAAAATCTAAGAACAAATTTCATTTTTGGGGAAGCCATTGGAGACATGGAGATGCATTGCTTTTTTCATTAGCATGTGCCCAG
upper sequence: AT5G51150.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G33510.1 (Glycine max), 3'ss of exon 3
----------------------------------gtacatctaatggtcatagtattgtctgtcgtacagagtaatatcaccacacagatgtttttttcggagtctgattttttctcttattaatagGCG-GCTTATAATTCCGCTAAGTCAAAGAACAAGTTCCATCTTTGGGGTAGCCATTGGAGACATGGAGATTCGTTACTTTTTTCTCTTGCATGTGCTCAG
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gtatttgaaagtgcatccccaaaatgatttctgagca-atatgatttacatggatgtatttaatgcttttt-tagtctcttgaaaatgatctgcatctgccaggctaatacatattcttgtatatcagTGTGCTTATAATTCTGCAAAATCTAAGAACAAGTTTCACCTTTGGGGGAGTCATTGGAGACATGGAGATTCATTGCTGTTTGCCCTTGCTTGTGCACAG
upper sequence: AT5G51150.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G34070.1 (Glycine max), 3'ss of exon 3
------------------------------gtacatctaatgg-tcatagtattgtctgtcgtacagagtaatatcaccaca--cagatgtttttttcggagtctgattttttctcttattaatagGCGGCTTATAATTCCGCTAAGTCAAAGAACAAGTTCCATCTTTGGGGTAGCCATTGGAGACATGGAGATTCGTTACTTTTTTCTCTTGCATGTGCTCAG
| ||| | | | | ||| | | | || || || | | || || | | | | | | |||| | || || ||||||||||| || || || || |||||||| || |||||||| || |||||||||||||||||||| || || ||| | ||||| ||||| |||
gtattcgaaagtgcatccccaaaatgatttctgagcgatatgacttacatttatgtatttaatgcattttagcctcttgaaaatcatctgcatctgctaggctaatacatattctttatataccagTGTGCTTATAATTCTGCAAAATCTAAAAACAAGTTTCACCTTTGGGGGAGTCATTGGAGACATGGAGATTCATTGCTGTTTGCCCTTGCTTGTGCACAG
upper sequence: AT5G51150.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv16s0039g02700.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------gtacatctaatggtcatagt-attgtctgtcgtacagagtaatatcaccacacagat---gtttttttcggagtctgattttttctcttattaatagGCGGCTTATAATTCCGCTAAGTCAAAGAACAAGTTCCATCTTTGGGGTAGCCATTGGAGACATGGAGATTCGTTACTTTTTTCTCTTGCATGTGCTCAG
||| | | | | | | | | | | || | || | || | || ||| ||| | | ||||| ||| | | || ||||| ||||| || ||||| ||||||||||| || || ||||| ||||||||||||||||||||||| ||||| ||| || | |||||||| |||
gtaaattaatatattttttattgcctcaattacttttcaaagctaaattgaatcgcaagagttaggggtttgctggtcatgctaatagggttcctttttctttttcctttttcctcccctcatcagTGTGCTTACAATTCTGCAAAGTCTAAGAACAAGTTTCACCTCTGGGGAAGCCATTGGAGACATGGAGATTCCTTACTCTTTGCTTTGGCATGTGCCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatatcaccacacagatgtttttttcggagtctgattttttctcttattaatagGCGGCTTATAATTCCGCTAAGTCAAAGAACAAGTTCCATCTTTGGGGTAGCCATTGGAGACATGGAGATTCGTTACTTTTTTCTCTTGCATGTGCTCAG
gtctgat putative branch site (score: 4)
tctgattttttctctt CT-rich tract
tgattttttctcttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacatctaatggtcatagtattgtctgtcgtacagagtaatatcaccacacagatgtttttttcggagtctgattttttctcttattaatagGCGGCTTATAATTCCGCTAAGTCAAAGAACAAGTTCCATCTTTGGGGTAGCCATTGGAGACATGGAGATTCGTTACTTTTTTCTCTTGCATGTGCTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT