Sequence
atgc intronic sequence ATGC exonic sequencegtacatctctgcttttcaatttcagatttctcagtttccaattgatatttcaaattatcatagaagatctatagggttggtttatgtttccgatgtggaacactgattttgcattacaatcagcgagtgaagagagaaaatactcatgattttgaattatacagGTTGATGCAGCTCTTGATCTCAGTCACACACAGAACATAGGAAGAATGATAAGAGCTCATTTCCCTCACTCGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G62410.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G62410.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GRMZM2G006452_T01 (Zea mays), 3'ss of exon 12
gtacatctctgcttttcaatttcagatttctcagtttccaattgatatttcaaattatcatagaagatctatagggttggtttatgtttccgatgtggaacactgattttgcattacaatcagcgagtgaagagagaaaatactcatgattttgaattatacagGTTGATGCAGCTCTTGATCTCAGTCACACACAGAACATAGGAAGAATGATAAGAGCTCATTTCCCTCACTCGCAG
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------------------------------------------------------ttacagtcttgtatgtctgatact--ctgatgcctcaaacgtttg-tacggattgtatgctgagagtgaccattttcaactga-----ctgatg--ttcgtgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAG
upper sequence: AT5G62410.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA12G36520.1 (Glycine max), 3'ss of exon 19
gtacatctctgcttttcaatttcagatttctcagtttccaattgatatttcaaattatcatagaagatctatagggttggtttatgtttccgatg--tggaacactgattttgcattacaatcagcg-agtgaagagagaaaatactcatgattttgaattatacagGTTGATGCAGCTCTTGATCTCAGTCACACACAGAACATAGGAAGAATGATAAGAGCTCATTTCCCTCACTCGCAG
| || || |||| || || | |||| | || || | | |||| || || |||| | |||| | || ||| | | | ||||||||||||||||||||| | || |||||||| |||||||| |||||||||| ||||| || || ||||| |||
--------------------------------------------------------------ataaattcat--ggttatttgataggtttgatggattgagcattctcgataaatta--ataggcatagtggttgggtcaaatgttaattgttt-aattcttgcagGTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATAAAGGCTCACTTTCCGCACTCTCAG
upper sequence: AT5G62410.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA13G27210.1 (Glycine max), 3'ss of exon 19
gtacatctctgcttttcaatttcagatttctcagtttccaattgatatttcaaattatcatagaagatctatagggttggtttatgtttccgatg--tggaacactgattttgcattacaatcagcga-gtgaagagagaaaatactcatgattttgaattatacagGTTGATGCAGCTCTTGATCTCAGTCACACACAGAACATAGGAAGAATGATAAGAGCTCATTTCCCTCACTCGCAG
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--------------------------------------------------------------ataaatttat--gcttgtttgataggattgatggattgagcattctcgataaatta--ataggcattgtggttgggtcaaatgttaattgtttc-attcttgcagGTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATAAAGGCTCACTTTCCGCACTCTCAG
upper sequence: AT5G62410.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: PP1S52_57V6.1 (Physcomitrella patens), 3'ss of exon 19
gtacatctctgcttttcaatttcagatttctcagtttccaattgatatttcaaattatcatagaagatctatagggttggtttatgtttccgatgtggaacactgattttgcattacaatcagcgagtgaagagagaaaatactcatgattttga-attatacagGTTGATGCAGCTCTTGATCTCAGTCACACACAGAACATAGGAAGAATGATAAGAGCTCATTTCCCTCACTCGCAG
| ||| || ||| |||| | ||| | | || | || ||| || | | | ||| | | || |||| | | ||||| || || ||||||||| | |||||||||||||||||||| |||||||| | || || || || |||||||||
--------------------------------------------------------------cataatccatttcaacc-tttctgttgcagatctatttaagagaaacggtata--aattttcgggacattggtaaaaggaattgtgtgcttgacgtcttgcagGTGGACGCTGCTCTTGATTTGAGTCACACACAGAACATAGGTAGAATGATCAAAGAACACTTTCCACACTCGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcattacaatcagcgagtgaagagagaaaatactcatgattttgaattatacagGTTGATGCAGCTCTTGATCTCAGTCACACACAGAACATAGGAAGAATGATAAGAGCTCATTTCCCTCACTCGCAG
atgattttgaattata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacatctctgcttttcaatttcagatttctcagtttccaattgatatttcaaattatcatagaagatctatagggttggtttatgtttccgatgtggaacactgattttgcattacaatcagcgagtgaagagagaaaatactcatgattttgaattatacagGTTGATGCAGCTCTTGATCTCAGTCACACACAGAACATAGGAAGAATGATAAGAGCTCATTTCCCTCACTCGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA