Sequence
atgc intronic sequence ATGC exonic sequence...cgtggtgagatcaggccttacttatacagttatatgtagaagatggattattgtgaaaatacctcaactcttaaattgacttggtactgatccccaacagGTATTTTATTATGCACCAAAGATGATTGAGAGCTGGAAGGGTCTGAAACTTCTTTCAAGGGCGGAATTTCACGTTGGTGCCCATGTGTCAAAGTTCCTAC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G51660.1 |
intron # | 24 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G51660.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GRMZM2G118697_T01 (Zea mays), 3'ss of exon 1
cgtggtgagatcaggccttacttatacagtt-atatgtagaagatggattattgtgaa--aatacctcaactcttaaattgacttggtactgatccccaacagGTATTTTATTATGCACCAAAGATGATTGAGAGCTGGAAGGGTCTGAAACTTCTTTCAAGGGCGGAATTTCACGTTGGTGCCCATGTGTCAAAGTTCCTAC
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-aatttttttttgtgtcttattcagaatttcgatatttttcag-tggaacacaaggatttggcccttcattacattatttga-ttaatgatgacaccttgcagATTTTCTATTATGCCCCCAAAATGGTGGAGAGCTGGAAGGGGCAAAAGCTCCTTTCCAGAGCAGAATTTCATGTTGGAGCCCATGTGTCGAAGTTTCTGA
upper sequence: AT5G51660.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GLYMA09G28030.1 (Glycine max), 3'ss of exon 24
cgtggtgagatcaggccttacttatacagttatatgtagaagatggattattgtgaaaatacctcaactcttaa-----attgacttggtactga-tccccaacagGTATTTTATTATGCACCAAAGATGATTGAGAGCTGGAAGGGTCTGAAACTTCTTTCAAGGGCGGAATTTCACGTTGGTGCCCATGTGTCAAAGTTCCTAC
||| | | | | || |||| || | ||| || | | || || | | || || ||| | | || | ||||| | ||||| ||||||||||||||| |||||| ||||| || | ||| ||||||||||| || |||||||| ||||||||||||||| | || ||| ||
-----tgaaagctgtatctgaagttatcattat-tgagtcgtgtttatttttattttattatcttttttgtcaagacatataacctttgaaatgtctggtgaacagATTTTTTACTATGCACCAAAGATGTCTGAGAGTTGGAAAGGACAGAAGCTTCTTTCAAGAGCTGAATTTCATGTTGGTGCCCATGTGACTAAATTCTTAA
upper sequence: AT5G51660.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GLYMA16G32890.1 (Glycine max), 3'ss of exon 24
--cgtggtgagatcaggccttacttatacagttatatgtagaagatggattattgtgaaaatacc-tcaactcttaaattgacttggtactgatccccaacagGTATTTTATTATGCACCAAAGATGATTGAGAGCTGGAAGGGTCTGAAACTTCTTTCAAGGGCGGAATTTCACGTTGGTGCCCATGTGTCAAAGTTCCTAC
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cttcccctcagttctttctatatttataattgtgtttatttttattttattatcttgtccttttcgtcaagacataaccttctaaatgtctggtg---agcagATTTTTTACTATGCCCCAAAGATGTCTGAGAGTTGGAAAGGACAGAAGCTTCTTTCAAGAGCTGAATTTCATGTTGGTGCCCATGTGACTAAATTCTTAA
upper sequence: AT5G51660.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: Vv16s0022g01860.t01 (Vitis vinifera), 3'ss of exon 24
cgtggtgagatcaggccttacttatacagttatatgt-agaagatggattattgtgaaaatacctcaactcttaaattgacttggtac-tgatcccca---acagGTATTTTATTATGCACCAAAGATGATTGAGAGCTGGAAGGGTCTGAAACTTCTTTCAAGGGCGGAATTTCACGTTGGTGCCCATGTGTCAAAGTTCCTAC
||| | | | || | || ||||| || || || | | | | | | | | || || | | ||| || ||||| |||| |||| |||||||||||||||||| || || ||||| || | ||| ||||||||||| || || ||||| ||||||||||||||| | |||||| | |
--ctttgattctaa---taaattgaaagattttatgtgagtaggcggcatgaggatttagttctttgaattttgttttaatattttacatgtaccccatctacagATATTCTATTATGCACCAAAGATGTCAGAAAGTTGGAAAGGACAGAAGCTTCTTTCAAGAGCTGAGTTTCATGTTGGTGCCCATGTGACTAAGTTCTTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattattgtgaaaatacctcaactcttaaattgacttggtactgatccccaacagGTATTTTATTATGCACCAAAGATGATTGAGAGCTGGAAGGGTCTGAAACTTCTTTCAAGGGCGGAATTTCACGTTGGTGCCCATGTGTCAAAGTTCCTAC
tactgat putative branch site (score: 2)
tcccc CT-rich tract
tcttaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgtggtgagatcaggccttacttatacagttatatgtagaagatggattattgtgaaaatacctcaactcttaaattgacttggtactgatccccaacagGTATTTTATTATGCACCAAAGATGATTGAGAGCTGGAAGGGTCTGAAACTTCTTTCAAGGGCGGAATTTCACGTTGGTGCCCATGTGTCAAAGTTCCTAC
- - - - - - - - - - - - - - - - - - tagaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaata