Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttgtaattatgcacttttcctgccagagttgctttcttgatctttgcattatccatttatatgttgggaactggtttacagGAGATGGATGGTTTTGACAGTAGCTCTGCAGTTATTGTTCTTGGAGCTACCAATCGAGCTGATGTCTTAGACCCTGCCCTGCGTCGGCCTGGGAGATTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G58870.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g43350.1 (Oryza sativa), 3'ss of exon 6
---------------------gtaagtttgtaattatgcac---ttttcctgccagagttgctttcttgatct--------ttgcattatccatttatatgttgggaactggtttac--agGAGATGGATGGTTTTGACAGTAGCTCTGCAGTTATTGTTCTTGGAGCTACCAATCGAGCTGATGTCTTAGACCCTGCCCTGCGTCGGCCTGGGAGATTTG
||| |||| ||| || |||| || || | | | || | ||| |||||| | | || | ||| |||| |||||||| ||||||| | ||| || || ||||| |||||||| || || ||||| ||||| ||||| |||||||| || || |||||||||||||
gtattgatagtaaagagtcctttaatcttgtgattctgactatattttactcacatacacacatctttagttggggtccaattgaattatcttcgtgttaattttctctgaatctacctagGAAATGGATGGATTTGACACCAACTCAGCTGTCATTGTACTTGGAGCAACAAACCGAGCAGATGTTTTAGATCCTGCCCTCCGACGCCCTGGGAGATTTG
upper sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA14G37090.1 (Glycine max), 3'ss of exon 7
--------------------gtaagtttgtaattatgcacttttcctgccagagttgctttcttgatctttgcattatccatttatatgttgggaactggtttacagGAGATGGATGGTTTTGACAGTAGCTCTGCAGTTATTGTTCTTGGAGCTACCAATCGAGCTGATGTCTTAGACCCTGCCCTGCGTCGGCCTGGGAGATTTG
| ||||| || | |||| | | | | | || | || | ||||| || ||||||||||||||||||||||| || ||||| || |||||||||||||| || ||||| || ||||||||||||||||| || || | || || |||||||
gttagcatttttccatattcattttcttgtatttttcttttttttttttttgggggggggggggggggggggcccaaaggggctaacgtcttaaaactgcattgcagGAGATGGATGGTTTTGACAGCAGTTCTGCTGTCATTGTTCTTGGAGCAACTAATCGTGCAGATGTCTTAGACCCTGCACTCCGAAGACCAGGAAGATTTG
upper sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G39040.1 (Glycine max), 3'ss of exon 7
------------gtaagtttgtaattatg-cacttt-tcctgccagagttgctttcttgatctttg---cattatccatttatatgttgggaactggtttacagGAGATGGATGGTTTTGACAGTAGCTCTGCAGTTATTGTTCTTGGAGCTACCAATCGAGCTGATGTCTTAGACCCTGCCCTGCGTCGGCCTGGGAGATTTG
| ||| | | || | ||| | || | || | ||| || || | || | ||||| || ||||||||||||||||||||||| || ||||| || |||||||||||||| || ||||| || ||||||||||||||||| || || | || ||||||||||
gttagcatttttccatgttcattttcttggtattttattttggggggactgggggagggggggttgtgtcacaatgagtctaacgtcttaaaactgcattgcagGAGATGGATGGTTTTGACAGCAGTTCTGCTGTCATTGTTCTTGGAGCAACTAATCGTGCAGATGTCTTAGACCCTGCACTCCGAAGACCAGGGAGATTTG
upper sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA0028S00210.1 (Glycine max), 3'ss of exon 6
----gtaagtttgtaattatgcacttttcctgccagagttgctttcttgatctttgcattatccatttatatgttggg-----------aactggtttacagGAGATGGATGGTTTTGACAGTAGCTCTGCAGTTATTGTTCTTGGAGCTACCAATCGAGCTGATGTCTTAGACCCTGCCCTGCGTCGGCCTGGGAGATTTG
| | | | | | |||| || | || || ||| | | | || || | ||| | || || ||||| |||||||| |||||||| | ||||| || ||||||||||||||||| ||| | | ||||||||||| ||||| || || ||||| || |||||||
gtcagcattcctttgacattttctgtttcttgtgaatgtaaagaaacaaatttttaagtaacactattgtaaggagggtaatttgttaaagttgcattgcagGAAATGGATGGGTTTGACAGCAATTCTGCGGTGATTGTTCTTGGAGCTACTAATAGGTCAGATGTCTTAGATCCTGCACTTCGCCGGCCAGGAAGATTTG
upper sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA18G07280.1 (Glycine max), 3'ss of exon 6
------gtaagtttgtaattatgcacttttcctgcc-----agagttgctttcttgatc---tttgcattatcca--tttatatgttgggaactggtttacagGAGATGGATGGTTTTGACAGTAGCTCTGCAGTTATTGTTCTTGGAGCTACCAATCGAGCTGATGTCTTAGACCCTGCCCTGCGTCGGCCTGGGAGATTTG
| |||| ||| | || | || ||| | || || | | | ||| | || || |||| | || || |||||||||||||| ||||| || | ||| |||| ||||||||||||||||| ||||| | |||||||| || ||||| || || ||||| || |||||||
gtcagcattcctttgacattttctgtttcttgtggatgtaaagaaataaatttttaagtaaaactaccttaatgaggttaatttgttaa-agttgcattgcagGAGATGGATGGGTTTGATAGCAATTCTTCAGTGATTGTTCTTGGAGCTACTAATCGGTCAGATGTCTTGGATCCTGCACTTCGCCGGCCAGGAAGATTTG
upper sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 6
gtaagtttgtaatt-atgcacttttcctgccagagttgctttcttgatctttgcattatccattta-tatgttgggaactggtttacagGAGATGGATGGTTTTGACAGTAGCTCTGCAGTTATTGTTCTTGGAGCTACCAATCGAGCTGATGTCTTAGACCCTGCCCTGCGTCGGCCTGGGAGATTTG
||| |||| | | | | | || | || | | | || | | || | || | |||| | || | | || ||| | ||||| |||||||| ||||| || | |||||| ||||||||||||||||| || ||||| | ||||||||||| ||||| || || || |||||||||||||
gtaggtttctcctggaagttatctttcagcttctgaaa-tgttttaaccatttccttgttagtttaatgtgattgaaattgggctgcagGAAATGGATGGATTTGATAGCAACTCTGCTGTTATTGTTCTTGGAGCAACTAATCGTTCAGATGTCTTAGATCCTGCACTTCGCCGCCCTGGGAGATTTG
upper sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S10_296V6.1 (Physcomitrella patens), 3'ss of exon 9
-gtaagtttgta-attatgcacttttcctgccagagttgctttcttgatctttgcat------tatccatttatatgt-tgggaactg-gttta---cagGAGATGGATGGTTTTGACAGTAGCTCTGCAGTTATTGTTCTTGGAGCTACCAATCGAGCTGATGTCTTAGACCCTGCCCTGCGTCGGCCTGGGAGATTTG
||| || | || || |||| || | | ||| | | | ||| | | | | | | || || |||| |||||| ||||||| ||||| || ||||| | |||||||| ||||| |||||||||||||||||||| || || ||||| || | || ||||| ||||||
tgtagtcttatgcataatatacttgtcatctccatcaatttttggtaacatacacataccttttgctgtctcaaacgagcgataattgtgtttttatcagGAGCTGGATGGATTTGAGAGCAGCTCAACTGTTATTGTACTTGGGGCTACCAATCGAGCTGATGTTTTGGATCCTGCTCTTAGGCGACCTGGACGATTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttgctttcttgatctttgcattatccatttatatgttgggaactggtttacagGAGATGGATGGTTTTGACAGTAGCTCTGCAGTTATTGTTCTTGGAGCTACCAATCGAGCTGATGTCTTAGACCCTGCCCTGCGTCGGCCTGGGAGATTTG
tcttgat putative branch site (score: 4)
attatccatttatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttgtaattatgcacttttcctgccagagttgctttcttgatctttgcattatccatttatatgttgggaactggtttacagGAGATGGATGGTTTTGACAGTAGCTCTGCAGTTATTGTTCTTGGAGCTACCAATCGAGCTGATGTCTTAGACCCTGCCCTGCGTCGGCCTGGGAGATTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT