Sequence
atgc intronic sequence ATGC exonic sequencegtaaagctctatatattaaagaatagctcttcttagcttacttacaaattgtgaaataattcacttctttggttgtcatcaatagGTTGAAGTAAACGTTTTGACGGGAGAAACAACGATCCTGCGTACAGATATTATCTATGATTGTGGGAAGAGTCTCAATCCCGCTGTTGATTTAGGACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G20960.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G20960.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA02G44000.1 (Glycine max), 3'ss of exon 7
-----gtaa--agctctatatattaaagaatagctcttcttagcttactta---caaattgtga--aataattcacttctt--tggttgtcatcaat-agGTTGAAGTAAACGTTTTGACGGGAGAAACAACGATCCTGCGTACAGATATTATCTATGATTGTGGGAAGAGTCTCAATCCCGCTGTTGATTTAGGACAG
||| | ||||| || | | || |||| | | | || |||||| ||| ||| || |||| | ||| | | |||| ||| || | || |||| |||||||| | ||| ||||||||||||||||||||||| |||||||||| || ||||| ||||||||||||
ttctgctaatcaattctatttacaacacaagccatcttactgaatcaattgaaccaaattatgatgaatgatacactaaataatggacactgtttctcagGTGGAAATAGATCTTCTGACTGGAGAAACCAGATGTTTGCAGACAGATATTATCTATGATTGTGGACAGAGTCTCAACCCAGCTGTGGATTTAGGACAG
upper sequence: AT5G20960.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA02G44000.2 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------------------------------------gtaaagctctatatattaaagaatagctcttcttagcttact-----tacaaattgtgaaataattc-acttctttggttgtcatcaatagGTTGAAGTAAACGTTTTGACGGGAGAAACAACGATCCTGCGTACAGATATTATCTATGATTGTGGGAAGAGTCTCAATCCCGCTGTTGATTTAGGACAG
||| | || | | || || | || | | | | ||| || | | | |||| | | | | | | | |||| ||| | | || ||| |||||||| | | ||| ||||| ||||| ||||||||||| ||||||| || || ||||||||||||||||||
gtaggtcgtttttattttttgttccatatgcatatctcaaatcaaaatggtattttctctagttcattaataataacttctcttgaatgttaagtgataatgtcaaattttctcaaaaaccatgttactgaagtaattgagcctacttatcttatactgattctaaataatggaatttatttctcagGTGGAAATTGATCTTCTGAATGGAGAAACCAGATTTTTGCAAACAGACATTATTTATGATTGTGGACAGAGTCTAAACCCTGCTGTTGATTTAGGACAG
upper sequence: AT5G20960.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA14G04950.1 (Glycine max), 3'ss of exon 7
-----------------------------------------------------------------------------------------gtaaagctctatatattaaagaatagctcttcttagcttactta--caaattgtgaaataattcacttct--ttggttgtcatcaat----agGTTGAAGTAAACGTTTTGACGGGAGAAACAACGATCCTGCGTACAGATATTATCTATGATTGTGGGAAGAGTCTCAATCCCGCTGTTGATTTAGGACAG
| | | ||| | | | | || | | ||| | ||| || | ||| | | | || | || | || | | |||| ||| || | || ||| |||||||| | | ||| ||||||||||| || |||||||| ||||||| || || ||||| ||||||||||||
gtaagatggtttttttttctatgcatatctcaaatcaaagttgtattttctcaagttaattggtagttacttctcttgaatgttaagtgcttatgtcatattttcagacaagccatgttactgaagtaactaaaccaacttatcttatactgccatgctaaatagtggaaatgatttctcagGTGGAAATAGATCTTCTGAATGGAGAAACCAGATTTTTGCAAACAGATATTATTTACGATTGTGGACAGAGTCTAAACCCTGCTGTGGATTTAGGACAG
upper sequence: AT5G20960.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv18s0041g02410.t01 (Vitis vinifera), 3'ss of exon 6
--------------gtaaagctctatatattaaagaatagctcttcttagcttact----tacaaattgtgaaataatt-cacttctttggttgtcatcaatagGTTGAAGTAAACGTTTTGACGGGAGAAACAACGATCCTGCGTACAGATATTATCTATGATTGTGGGAAGAGTCTCAATCCCGCTGTTGATTTAGGACAG
| || | | | ||| ||| ||| | | || | ||| || | ||||| | |||| ||||| |||| || ||||| || | || ||| |||| || || ||| | |||||||| ||||| ||||| |||||||||| || ||||| ||||||||||||
attaagttagtattcttcaggtaaacttggaggagactaggctttcatgcttaaccatgcttcaatttttactataataatgaaacattgggtgtcac----agGTGGAGGTAAATCTTCTCACTGGACAAACCACAATTTTGCAATCTGATATTATATATGACTGTGGTCAGAGTCTCAACCCTGCTGTGGATTTAGGACAG
upper sequence: AT5G20960.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv18s0041g02430.t01 (Vitis vinifera), 3'ss of exon 7
----------------------------------------------------------------gtaaagctctatatattaaagaatagctcttcttagcttact----tacaaattgtgaaataatt-cacttctttggttgtcatcaatagGTTGAAGTAAACGTTTTGACGGGAGAAACAACGATCCTGCGTACAGATATTATCTATGATTGTGGGAAGAGTCTCAATCCCGCTGTTGATTTAGGACAG
| || | | || ||| ||| ||| | | || | ||| || | ||||| |||||| ||||| |||| || ||||| || | || ||| |||| || || ||| | |||||||| ||||| ||||| |||||||||| || ||||| ||||||||||||
gcaagtttttcaagatcccattaattcctctccatagagtttttattgaaattaagttagtattcttcaggtaaacatggaggagagtaggctttcatgcttaaccatgcttcaatttttactataataatgaaactttgggtgtcac----agGTGGAGGTAAATCTTCTCACTGGACAAACCACAATTTTGCAATCTGATATTATATATGACTGTGGTCAGAGTCTCAACCCTGCTGTGGATTTAGGACAG
upper sequence: AT5G20960.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv06s0009g00770.t01 (Vitis vinifera), 3'ss of exon 7
---------------------------------------------------------------------------------------------gtaaagctctatatattaaagaatagctct-tcttagcttacttacaaat---tgtgaaataatt-cacttctttggttgtcatcaatagGTTGAAGTAAACGTTTTGACGGGAGAAACAACGATCCTGCGTACAGATATTATCTATGATTGTGGGAAGAGTCTCAATCCCGCTGTTGATTTAGGACAG
| ||| || | ||| || || || | || | | |||| |||| ||||| ||||| |||| || ||||| || | || |||||||| || || ||| | |||||||| ||||| |||||| |||| ||||| || ||||| ||||||||||||
gcaagttttttgagattgcctaaaccactttaattattgtttttgttggagttaaattagtgctcttcatgttaacttggagaagactaagcttgcaggcttaatgatgcatcaaattttactatcaaggccgatatatagttatgtgtgtgctaataatgaaactttgagtgtcac----agGTGGAGGTAAATCTTCTCACTGGAGAAACCACCATTTTGCAATCTGATATTATATATGACTGTGGGCAGAGCCTCAACCCTGCTGTGGATTTAGGACAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|116475730|gb|EG518322.1|EG518322EST: TGCCTGACTCCACTGGCGAATACCTGAACTATGGAATTGCAGCGAGCGAG GTTGAAGTAAACGTTTTGACGGGAGAAACAACGATCCTGCGTACAGATATT
genomic: TGCCTGACTCCACTGGCGAATACCTGAACTATGGAATTGCAGCGAGCGAGgtaaagctct ... tcatcaatagGTTGAAGTAAACGTTTTGACGGGAGAAACAACGATCCTGCGTACAGATATT
EST:
gi|125041037|gb|EL113306.1|EL113306EST: TTGCAGCGAGCGAG GTTGAAGTAAACGTTTTGACGGGAGAAACAACGATCCTGCGTACAGATATT
genomic: TTGCAGCGAGCGAGgtaaagctct ... tcatcaatagGTTGAAGTAAACGTTTTGACGGGAGAAACAACGATCCTGCGTACAGATATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttagcttacttacaaattgtgaaataattcacttctttggttgtcatcaatagGTTGAAGTAAACGTTTTGACGGGAGAAACAACGATCCTGCGTACAGATATTATCTATGATTGTGGGAAGAGTCTCAATCCCGCTGTTGATTTAGGACAG
tacttac putative branch site (score: 1)
aaattgtgaaataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagctctatatattaaagaatagctcttcttagcttacttacaaattgtgaaataattcacttctttggttgtcatcaatagGTTGAAGTAAACGTTTTGACGGGAGAAACAACGATCCTGCGTACAGATATTATCTATGATTGTGGGAAGAGTCTCAATCCCGCTGTTGATTTAGGACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT