Sequence
atgc intronic sequence ATGC exonic sequence...gtcgtaaggctatctggaatagttttttttttctggattatgttttggttgaagcttggctttgacgagtttttgactgacagtctaccctgaaatacagGTCTACACTGTGGGTCCCGAATATGCACACGCTGAAGCAAGAAAATCACCTGTTGTTGATGGTGTAGTAATGAGAAATCCAGATGGGAAGGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G15070.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G15070.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 8
gtcgtaaggctatctggaatagttttttttttctggattatgttttggttgaagcttggctttgacgagtttttgactga--cagtctaccctgaaatacagGTCTACACTGTGGGTCCCGAATATGCACACGCTGAAGCAAGAAAATCACCTGTTGTTGATGGTGTAGTAATGAGAAATCCAGATGGGAAGGAA
| | | ||| | ||| | | ||| || | || || || |||| | | || | || | | | | | ||||| ||||| || || || | ||||||||| ||||| ||| | |||||||| |||||||||||||| || ||||| || || |||||||| |||
tttggagagcttttgcattgagtaaatcatgcagggaacatatgttc-caaaaatttcacttttctg-gcttccgtctaaattatcacaaaactattttcagGTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAA
upper sequence: AT5G15070.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 6
--------gtcgtaaggct-atctggaata--gttttttttttctggattatgttttggttgaagcttgg----ctttgacgagtt---tttgactgacagtctaccctgaaata----cagGTCTACACTGTGGGTCCCGAATATGCACACGCTGAAGCAAGAAAATCACCTGTTGTTGATGGTGTAGTAATGAGAAATCCAGATGGGAAGGAA
|| | || | || | | | || |||| ||| | | | ||| | || || |||| | || | | || || | | |||| |||| || || || ||||| |||||||| || ||||| ||||| || || ||||||||||||||||| || ||||||||||| |||||||||||
gtttggcagttttgagatttatgttgctttctattccttttctcttaaatgtatttggaatgtttctccatatcctttagcatattagaatggtctcctagaattttcataaatgactgtagGTGTATACAGTAGGTCCTGAATATGCGCATGCTGAGGCAAGGAAGTCTCCTGTTGTTGATGGTGTTGTTATGAGAAATCCTAATGGGAAGGAA
upper sequence: AT5G15070.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 8
--------gtcgtaaggct----atctggaatagttttttttttctggattatgttt----tggttgaagcttggctttgacgagttt---ttgactgacagtctaccctgaaata---cagGTCTACACTGTGGGTCCCGAATATGCACACGCTGAAGCAAGAAAATCACCTGTTGTTGATGGTGTAGTAATGAGAAATCCAGATGGGAAGGAA
|| | || | || || |||||||| ||| | | | ||| || ||| | |||| | || | | || || | | |||| |||| || || || ||||| |||||||| || ||||| ||||| || || ||||||||||||||||| || |||||||||| ||||||||||||
gtttggctgttttgagatttataatgctttctatttttttttctcttaaatgtatttggaatgtttgtccatatcctttagcatattagaatggtctcttagaattttcataaatgacttagGTGTATACAGTAGGTCCTGAATATGCGCATGCTGAGGCAAGGAAGTCTCCTGTTGTTGATGGTGTTGTTATGAGAAATCTTGATGGGAAGGAA
upper sequence: AT5G15070.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 8
--------------------------------------------------gtcgtaaggctatctggaatagttttttttttctggat-tatgttttggttgaagcttggctttgacga-----gtttttgactgacagtctaccctgaaat-acagGTCTACACTGTGGGTCCCGAATATGCACACGCTGAAGCAAGAAAATCACCTGTTGTTGATGGTGTAGTAATGAGAAATCCAGATGGGAAGGAA
| | ||| | | ||||||||| || |||| || || | | | ||| || | || || | ||| | | | | || |||| || || || || || |||||||| || ||||| ||||| || || ||||| ||||||||||| || ||||||||||| ||||||||||||
gtttgactatgaagtttatgttgctttgtgtttattttattgtttctttatttttttaattatatatttgggcttttttttttcagacacatgtgatgtttctacatagtttttcacaatagaaattcttttcaaacattttgacatatgattgtagGTATATACAGTTGGCCCTGAATATGCTCATGCTGAGGCAAGGAAGTCTCCTGTGGTTGATGGTGTTGTGATGAGAAATCCTGATGGGAAGGAA
upper sequence: AT5G15070.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 6
--------------------------------------------------gtcgtaaggctatctggaatagttttttttttctggattatgttttggttgaagcttggctttgac----gagtttttgactgacagtctaccctg-aaatacagGTCTACACTGTGGGTCCCGAATATGCACACGCTGAAGCAAGAAAATCACCTGTTGTTGATGGTGTAGTAATGAGAAATCCAGATGGGAAGGAA
| | ||| | | | | |||||| | | |||||| || || | | | ||| || || || | ||| | | | | | | |||| || || || || || |||||||| || ||||| ||||| || || ||||| ||||||||||| || ||||||||| | ||||||||||||
gtttggctgtgaagtttatgttgctttgtgtttgttttattgtttctttatttttttaattatatatatttgggatttttt-cagacttatgtgatgtttctaaatagtttttcacaacagaaattattttcaacatttcaacatatgattgtagGTATATACAGTTGGCCCTGAATATGCTCATGCTGAGGCAAGGAAGTCTCCTGTGGTTGATGGTGTTGTGATGAGAAATACTGATGGGAAGGAA
upper sequence: AT5G15070.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 8
gtcgtaaggctatctggaatagtttttt-ttttctggattatgttt-tggttgaagcttggctttgacgagtttttgactgacagtctaccc--tgaaatacagGTCTACACTGTGGGTCCCGAATATGCACACGCTGAAGCAAGAAAATCACCTGTTGTTGATGGTGTAGTAATGAGAAATCCAGATGGGAAGGAA
|||| | || |||| |||| || | || || || | || | || ||| | | |||| | ||| | | | | |||| || || || || || ||||||||||| ||||| ||||| || || |||||||||||||| || || |||||||| || |||||||| |||
-atgtaa---tgcctatggtagtcttttgccttttccatcattttcatttttcactttttatttttatcatcagttgatcaagcttcttgtcaatttataatagGTGTATACAGTTGGCCCTGAATATGCACATGCTGAGGCAAGGAAGTCTCCTGTTGTTGATGGCGTTGTTATGAGAAACCCCGATGGGAAAGAA
upper sequence: AT5G15070.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S70_284V6.1 (Physcomitrella patens), 3'ss of exon 8
-gtcgtaaggctatctggaatagtttttttttt--ctggattatgttttggttgaagcttggctttgacgagtttttgactgacagtctaccctgaaatacagGTCTACACTGTGGGTCCCGAATATGCACACGCTGAAGCAAGAAAATCACCTGTTGTTGATGGTGTAGTAATGAGAAATCCAGATGGGAAGGAA
|| | | ||| |||| | || || || || ||| | | ||| |||| || ||||| || | | ||||| ||||| ||||| || |||||||| || || ||||| ||||||| ||||||||||| || ||||| ||||||| | |||| ||||||||
aaaaaaaattcgttgtggtggagttcgtagttgaatcgggaaataaccgtgtgcaagttcgcaagtga-gagtgttcatgtgacaacct--ttgggcgtgcagGTGTACACAGTGGGACCAGAATATGCCCATGCAGAAGCTCGAAAATCTCCTGTTGTTGACGGGGTAGTTATGAGAAGTGCAGACGGGAAGGAG
upper sequence: AT5G15070.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S112_67V6.1 (Physcomitrella patens), 3'ss of exon 8
--gtcgtaaggctatctggaatagttttttttttctggattatgttttggttgaagcttggctttgacgagtttttgactgaca--gtctacc-ctgaaatacagGTCTACACTGTGGGTCCCGAATATGCACACGCTGAAGCAAGAAAATCACCTGTTGTTGATGGTGTAGTAATGAGAAATCCAGATGGGAAGGAA
|| ||| | | || ||| | | | | | | || |||| | |||||| || | | ||| || | | || || ||||| || || ||||| || |||||||| || || ||||| ||||| || |||||||| ||||||||||||||||||| | | ||||| |||||
acatctgttagct-ttggcaaggactttggtcgattcgcctttttcatgtgtgaatttcaa----gacgagattgttgccgacgtggtatgcttcttgcatgcagGTGTATACAGTGGGGCCAGAATATGCTCATGCAGAAGCTAGAAAGTCTCCTGTTGTGGATGGTGTAGTAATGAGAAGTGCTGATGGAAAGGAG
upper sequence: AT5G15070.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ19878 (Selaginella moellendorffii), 3'ss of exon 8
gtcgtaaggctatctggaatagttttttttttctggattatgttttggttga-agcttggctttgacgagtttttgactgacagtctaccctgaaatacagGTCTACACTGTGGGTCCCGAATATGCACACGCTGAAGCAAGAAAATCACCTGTTGTTGATGGTGTAGTAATGAGAAATCCAGATGGGAAGGAA
|| || | || ||| | ||| || | | | || ||||| | ||||| |||||||| || || |||||||| || ||||| ||| ||||||||||||||||||| || || || |||||| ||| ||||| || ||
-----------------------------------------------gtagacaactcaactt---cttgttcttagc-agccgcctcttctgaactgcagGTATACACTGTTGGACCAGAATATGCTCATGCTGAGGCACGAAAATCACCTGTTGTTGACGGGGTTGTTTTGAGAAGTCCCGATGGAAAAGAG
upper sequence: AT5G15070.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ07403 (Selaginella moellendorffii), 3'ss of exon 8
gtcgtaaggctatctggaatagttttttttttctggattatgttttggttga-agcttggctttgacgagtttttgactgacagtctaccctgaaatacagGTCTACACTGTGGGTCCCGAATATGCACACGCTGAAGCAAGAAAATCACCTGTTGTTGATGGTGTAGTAATGAGAAATCCAGATGGGAAGGAA
|| || | || ||| | ||| || | | | | || ||||| | ||||| |||||||| || || |||||||| || ||||| ||| ||||||||||||||||||| || || || |||||| ||| ||||| || ||
-----------------------------------------------gtagacaactcaactt---cttgttcttagcagtc-gcctcttctgaactgcagGTATACACTGTTGGACCAGAATATGCTCATGCTGAGGCACGAAAATCACCTGTTGTTGACGGGGTTGTTTTGAGAAGTCCTGATGGAAAAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggttgaagcttggctttgacgagtttttgactgacagtctaccctgaaatacagGTCTACACTGTGGGTCCCGAATATGCACACGCTGAAGCAAGAAAATCACCTGTTGTTGATGGTGTAGTAATGAGAAATCCAGATGGGAAGGAA
gactgac putative branch site (score: 2)
tctaccct putative PPT
agttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcgtaaggctatctggaatagttttttttttctggattatgttttggttgaagcttggctttgacgagtttttgactgacagtctaccctgaaatacagGTCTACACTGTGGGTCCCGAATATGCACACGCTGAAGCAAGAAAATCACCTGTTGTTGATGGTGTAGTAATGAGAAATCCAGATGGGAAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA