Sequence
atgc intronic sequence ATGC exonic sequence...ttacatgcactcttgtttgtcagatacataaacttgtcatcatagcctatataagaatcatgcttatactaatatttctctgtttatgatatatttgcagGTGAATCCTTCTGACGTTATAATTCTGGAAGGTATACTCATTTTCCATGACCCTCGGGTGCGAGATTTGATGAACATGAAGATATTTGTAGACGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G55810.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 3'ss of exon 5
-------ttacatgcactcttgtttgtcagatacataaacttgtcatcatagcctatataagaatcatgcttatactaatatttctctgtttatgatatatttgcagGTGAATCCTTCTGACGTTATAATTCTGGAAGGTATACTCATTTTCCATGACCCTCGGGTGCGAGATTTGATGAACATGAAGATATTTGTAGACGCAG
||| || |||| | | || | | | | | || | | | | | ||| || | | | | ||| ||| | | ||||| |||||||| || || || ||| |||||||||| || |||||||||| | || || || || ||||||||||||||||||||||| || |||
aagaaaattagat-cactgcttatagtttgttcttcactttatttattcatatttgttttact-ttatgttt---cagagaccctaatattt-tgac-tgctgtcagGTCAATCCTTCAGATGTAATTATTTTGGAAGGTATTCTGGTTTTCCATGATTCACGTGTCCGGGACTTGATGAACATGAAGATATTTGTTGATACAG
upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 5
-ttacatgcactct---tgtttgtc-agatacataaacttgtcatcatagcctatataagaatcatgcttatactaatatttctctgtttatgatatatttgcagGTGAATCCTTCTGACGTTATAATTCTGGAAGGTATACTCATTTTCCATGACCCTCGGGTGCGAGATTTGATGAACATGAAGATATTTGTAGACGCAG
| | || || | | || | ||| | || ||||| || | | || | | | |||| || || | | | | | |||| | ||| |||||||| ||||| || ||||||||| ||||||| || || ||||||||||||| || || || || |||||||| |||||||||||||| ||| |||
ataaaatacattttacatgatagtccaaatgcataatttt-tagtttta--caaagttgttgtcattctcatttcattttgtgttgccttat--cgtgttttcagGTGAACCCTTCAGATGTTATAATTTTGGAAGGCATCCTTGTTTTCCATGACCCACGTGTTCGGGAGTTGATGAATATGAAGATATTTGTTGACACAG
upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 5
ttacatgcactcttg-tttgtcagatacataaacttgtcatcatagcctatataagaatcatgcttatactaatatttctctgtttatgatatatttgcagGTGAATCCTTCTGACGTTATAATTCTGGAAGGTATACTCATTTTCCATGACCCTCGGGTGCGAGATTTGATGAACATGAAGATATTTGTAGACGCAG-
||| | || || | | || || |||| | | | | | |||| || || | | | | | ||||| || ||| |||||||| ||||| || ||||||||| | ||||| || || |||||||||| || || || || || |||||||| |||||||||||||| ||| |||
aagcatagaatcatgatattccaaatgcatattttagcttagttttatgaagttgctgtcattctcatttcattttgtgttgctttat--catgttttcaggTGAACCCTTCAGATGTTATAATTTTAGAAGGCATCCTTGTTTTCCATGATCCACGTGTTCGGGAGTTGATGAATATGAAGATATTTGTTGACACAGG
upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 5
ttacatgcactcttgtttgtcagatacataaacttgtcatcatagcctatataagaatcatgcttatactaatatttc---tctgtttatgatatatttgcagGTGAATCCTTCTGACGTTATAATTCTGGAAGGTATACTCATTTTCCATGACCCTCGGGTGCGAGATTTGATGAACATGAAGATATTTGTAGACGCAG
| | ||||| | | | | ||| | || | || ||| | | ||| ||||| ||| | ||||| | | ||||||||| || || | || ||||| ||| |||||||||| || |||| ||||| || || ||||||| |||||||| |||||||||||||| ||| |||
-catgtttcttcttgcgttttatctccattagagtggaaatttatatggaatacaatttcagct-atacttcccttttatgttggtttaatctgt-tttgcagGTAAACCCAGCGGATGTTATTATTTTGGAAGGTATCCTTGTTTTTCATGATCCACGAGTGCGAGCATTGATGAATATGAAGATATTTGTTGACACAG
upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 5
ttacatgcactcttgtttgtcagatacataaacttgtcat-catagcctatataagaatcatgcttatactaatatttctctgt-ttatgatatatttg-cagGTGAATCCTTCTGACGTTATAATTCTGGAAGGTATACTCATTTTCCATGACCCTCGGGTGCGAGATTTGATGAACATGAAGATATTTGTAGACGCAG
| || || | || | || | | | | | | | | | | | | | ||| | ||||| ||||||| ||||| || ||||| || || |||||| ||||||| ||||||||||| ||||| | ||| || || || ||||||||||||||||||||||| || |||
---agggtggtcctgaatcctgtgagattatatttcaggtacttgatttctgttcccgggttacatgcattgagaaccctcattgctatgaaatatttggcagGTCAACCCTTCAGATGTGATAATTTTGGAAGGCATACTCATTTTTCATGATCTTCGTGTCCGGGAATTGATGAACATGAAGATATTTGTTGATACAG
upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ31180 (Selaginella moellendorffii), 3'ss of exon 4
ttacatgcactcttgtttgtcagatacataaacttgtcatcatagcctatataagaatcatgcttatactaatatttctctgtttatgatatatttgc--agGTGAATCCTTCTGACGTTATAATTCTGGAAGGTATACTCATTTTCCATGACCCTCGGGTGCGAGATTTGATGAACATGAAGATATTTGTAGACGCAG
| | | ||| | | || | | || ||||| |||||||| | | || |||||||| |||||||| || || ||||||||||| ||| || || ||| |||||||||||||||| ||||| ||| |||
------------------------------------------------gtctgtgcatctt-ttcatccatgcacagtctgaagagccatggttttgcctagGTGAATGCAGCAGATGTTATAATCCTGGAAGGAATCCTGGTTTTCCATGACAGTCGCGTTCGTGATCTGATGAACATGAAGATTTTTGTCGACACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctatataagaatcatgcttatactaatatttctctgtttatgatatatttgcagGTGAATCCTTCTGACGTTATAATTCTGGAAGGTATACTCATTTTCCATGACCCTCGGGTGCGAGATTTGATGAACATGAAGATATTTGTAGACGCAG
tactaat putative branch site (score: 1)
taatatttctctgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttacatgcactcttgtttgtcagatacataaacttgtcatcatagcctatataagaatcatgcttatactaatatttctctgtttatgatatatttgcagGTGAATCCTTCTGACGTTATAATTCTGGAAGGTATACTCATTTTCCATGACCCTCGGGTGCGAGATTTGATGAACATGAAGATATTTGTAGACGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- acatgca
- - - - - - -tgtttgt
- - - - - - - - - - - - - cataaac
- - - - - - - - - - - - - - - - - - - - - - - - - - -agaatca