Sequence
atgc intronic sequence ATGC exonic sequencegtacatctcgattttccatttccatgaatcattgctcttcctttgcattttcaatacgtaacgactaaattcgtgttgacagtgatcttgaaatgttcacaatcacatgatcttgttgagtttgatgacataagagaagtcatgactttatttttatcagGTTGATGCAGCTCTTGATCTAAGCCACACACAGAACATAGGAAGAATGATAAAATCTCATTTCCCACATTCACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G47460.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G47460.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GRMZM2G006452_T01 (Zea mays), 3'ss of exon 12
gtacatctcgattttccatttccatgaatcattgctcttcctttgcattttcaatacgtaacgactaaattcgtgttg-acagtgat-cttgaaatgttcacaatcacatgatcttgttgagtttgatgacataagag-aagtcatgactttatttttatcagGTTGATGCAGCTCTTGATCTAAGCCACACACAGAACATAGGAAGAATGATAAAATCTCATTTCCCACATTCACAG
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----------------------------------------------------------ttacagtcttgtatgtctgatactctgatgcctcaaacgtttgta--cggattgtat-gctgagagtgaccattttcaactgactgatg--ttcgtgctctgcagGTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAG
upper sequence: AT3G47460.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA12G36520.1 (Glycine max), 3'ss of exon 19
gtacatctcgattttccatttccatgaatcattgctcttcctttgcattttcaatacgtaacgactaaattcgtgttgac--agtgatcttgaaatgttca-caatcacatgatcttgttgagtttgatgacataagagaagtcatgact--ttatttttatcagGTTGATGCAGCTCTTGATCTAAGCCACACACAGAACATAGGAAGAATGATAAAATCTCATTTCCCACATTCACAG
||||||| || | | | |||| || | || || | | || | | | || | | || | | | | ||| || | ||||||||||||||||||||| | ||||||||||| |||||||| ||||||||||| |||| || || || || |||
----------------------------------------------------------------ataaattcatggttatttgataggtttgatggattgagcattctcgataaattaataggcatagtggt-tgggtcaaatgttaattgtttaattcttgcagGTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATAAAGGCTCACTTTCCGCACTCTCAG
upper sequence: AT3G47460.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA13G27210.1 (Glycine max), 3'ss of exon 19
gtacatctcgattttccatttccatgaatcattgctcttcctttgcattttcaatacgtaacgactaaattcgtgttgacagtgatcttgaaatgttcacaatcacatgatcttgttgagtttgatgacataagagaagtca-tgactttatttttatcagGTTGATGCAGCTCTTGATCTAAGCCACACACAGAACATAGGAAGAATGATAAAATCTCATTTCCCACATTCACAG
||| || | || |||| || | || | || || || || | | | | ||| | | | || | | || ||| || ||||||||||||||||||||| | ||||||||||| |||||||| ||||||||||| |||| || || || || |||
---------------------------------------------------------ataa-atttatgcttgt-ttgataggattgatggattgagcattctcg-ataaattaataggcattgtggttgggtcaaatgttaattgtttcattcttg-cagGTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATAAAGGCTCACTTTCCGCACTCTCAG
upper sequence: AT3G47460.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: Vv16s0022g00060.t01 (Vitis vinifera), 3'ss of exon 18
gtacatctcgattttccatttccatgaatcattgctcttcctttgcattttcaatacgtaacgactaaattcgtgttgacagtgatcttgaaatgttcacaatcacatgatcttgttgagtttgatgacataagagaagtcatgactttatttttatcagGTTGATGCAGCTCTTGATCTAAGCCACACACAGAACATAGGAAGAATGATAAAATCTCATTTCCCACATTCACAG
| | ||| || | || | || || || || || | |||| | | ||| | | ||| ||| || |||| ||||| || |||||| |||| ||||| || ||||| ||||||||||| ||||| |||||||||||||| |||
------------------------------------------------------gttttgttcatgaaagtcattttcccttctatattttgttgctct---atacttctacttgcatattcaaatggatctgcaaataatttgattttg---ttgatagGTCGATGCTGCCCTTGATTTAAGTCACACTCAAAACATTGGAAGAATGATTAAATCCCATTTCCCACATTCCCAG
upper sequence: AT3G47460.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: PP1S52_57V6.1 (Physcomitrella patens), 3'ss of exon 19
gtacatctcgattttccatttccatgaatcattgctcttcctttgcattttcaatacgtaacgactaaattcgtgttgacagtgatcttgaaatgttcacaatcacatgatcttgttgagtttgatgacataagagaagtcatg-actttatttttatcagGTTGATGCAGCTCTTGATCTAAGCCACACACAGAACATAGGAAGAATGATAAAATCTCATTTCCCACATTCACAG
||| | | | || || ||||| | || | | || || | || | | ||| || | | || ||| | | | ||||| || || ||||||||| | || ||||||||||||||||| |||||||| ||| || || ||||| || |||
-------------------------------------------------cataatccatttcaacc---tttctgttgcagatctatttaagaga-----aacggtataaattttcgggacattg----gtaaaaggaattgtgtgcttgacgtcttgcagGTGGACGCTGCTCTTGATTTGAGTCACACACAGAACATAGGTAGAATGATCAAAGAACACTTTCCACACTCGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catgatcttgttgagtttgatgacataagagaagtcatgactttatttttatcagGTTGATGCAGCTCTTGATCTAAGCCACACACAGAACATAGGAAGAATGATAAAATCTCATTTCCCACATTCACAG
gtttgat putative branch site (score: 5)
ctttattttt putative PPT
atgactttatttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacatctcgattttccatttccatgaatcattgctcttcctttgcattttcaatacgtaacgactaaattcgtgttgacagtgatcttgaaatgttcacaatcacatgatcttgttgagtttgatgacataagagaagtcatgactttatttttatcagGTTGATGCAGCTCTTGATCTAAGCCACACACAGAACATAGGAAGAATGATAAAATCTCATTTCCCACATTCACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA