Sequence
atgc intronic sequence ATGC exonic sequence...tctagaatcatttaaaaataattttcgattatctctagcattgctttttatacattgattactacataaatgaagatggttggtttgagttgtgtggcagGAGTCAGAGAAGGTAGCGTTGGCGGAATCAACGGGGTTAGATCAGAAACAAATCAACAATTGGTTCATAAACCAAAGAAAGCGTCACTGGAAACCATCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G08150.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G08150.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G028041_T01 (Zea mays), 3'ss of exon 4
tctagaatcatttaaaaataattttcgattatctctagcattgctttttatacattgattactacataaatgaagatggttggtttgagttgtgt---ggcagGAGTCAGAGAAGGTAGCGTTGGCGGAATCAACGGGGTTAGATCAGAAACAAATCAACAATTGGTTCATAAACCAAAGAAAGCGTCACTGGAAACCATCTG
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--ttccgtgacctttacgcgatgttaacactgcttcagaaccatgaactgaa-gcagaatgtattgtataacattgttactgatttaatgtttgttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAACGGCACTGGAAGCCATCGG
upper sequence: AT4G08150.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G05210.1 (Glycine max), 3'ss of exon 4
------------------------------------------------------------------------------tctagaatcatttaaa--aataatttt--cgattatctctagcattgctttttatacattgattactacataaatgaagat--ggttggtttgagttgtgtggcagGAGTCAGAGAAGGTAGCGTTGGCGGAATCAACGGGGTTAGATCAGAAACAAATCAACAATTGGTTCATAAACCAAAGAAAGCGTCACTGGAAACCATCTG
| || || |||| |||| ||| ||| || ||| | | | || ||| | || | | | || ||| | | | | |||| ||||||||||| ||| |||| ||| |||| || || |||||||| ||||| || || ||||||||||| ||||| || || |||||||||||||| |
gtatgtaaatttctaatttttagcttcatatatatatatatatatatgttatcgagttattcttatcttcaccttttatatattttctcttaatctaatagctttaacgaataactcatccttcagaactcatcaatttctctctctagatcttctgaataaattgttccgcgattaaccttagGAATCAGAGAAGGTGGCGCTGGCTGAAGCAACTGGTTTGGATCAGAAGCAAATAAATAACTGGTTCATAAATCAAAGGAAACGGCACTGGAAACCATCGG
upper sequence: AT4G08150.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G10430.1 (Glycine max), 3'ss of exon 4
tctagaatcatttaaaaataattttcgattatctctagcat-tgctttttatacattgattactacataaatgaagatggttggtttgagttg-tgtggcagGAGTCAGAGAAGGTAGCGTTGGCGGAATCAACGGGGTTAGATCAGAAACAAATCAACAATTGGTTCATAAACCAAAGAAAGCGTCACTGGAAACCATCTG
| || || | | ||||||| || | | | ||| || ||| ||| || ||| ||| | || | | | | || | | |||| ||||||||||| || ||||| |||||||| || || || || || ||||| || || |||||||||||||| || ||| | || |||||||||||||
-gtgaaaccacacatttacaattttcaataaattttgtcatatgtgtttgatatatatatttctaaa-aattatgtacttctcatggtggtcactactgtagGAATCAGAGAAGGTGGCATTGGCTGAATCAACTGGTTTGGACCAAAAGCAAATAAATAACTGGTTCATAAACCAGAGGAAGAGGCATTGGAAACCATCTG
upper sequence: AT4G08150.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA0041S00360.1 (Glycine max), 3'ss of exon 5
tctagaatcatttaaaaataattt-tcgatt---atctctagcattgctttttatacattgattactacataaatgaagatggttggtttgagttgt------gtggcagGAGTCAGAGAAGGTAGCGTTGGCGGAATCAACGGGGTTAGATCAGAAACAAATCAACAATTGGTTCATAAACCAAAGAAAGCGTCACTGGAAACCATCTG
|| | | | | ||| | ||| || ||| | | || ||| || ||| ||| | || || || | | | | | | |||| || |||||||| || ||||| |||||||| || || || || || ||||| || || ||||||||||||||||| ||| | || |||||||||||||
---------atattagagtgttttgttaattagcatttctcatagtatgcttgatatatacatttctaaa-aattgtgtatttctcatagtggatatttaatcattatagGAATCGGAGAAGGTTGCATTGGCTGAATCAACTGGTTTGGACCAAAAGCAAATAAATAACTGGTTCATAAACCAAAGGAAGAGGCATTGGAAACCATCTG
upper sequence: AT4G08150.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv18s0001g08380.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------------------------------------------------------tctagaatcatttaaaaataattttcgattatctctagcattgctttttatacattgattactacataaatgaagatggttggtttgagttgtgtggcagGAGTCAGAGAAGGTAGCGTTGGCGGAATCAACGGGGTTAGATCAGAAACAAATCAACAATTGGTTCATAAACCAAAGAAAGCGTCACTGGAAACCATCTG
| ||| | || | || | | | || | || || || || | | ||| | | ||| | | || | | | |||||| |||||||||| || ||||| ||| | || || || || ||||||||||| || |||||||||||||||||||| || | ||||||||||| ||||
gtatgcatatcctctttgacctgtatcctacacttggtcaaactgttagaatgatctttacataaaattctaaattggaacaaagtatatatgttactaaaaaatatttattgtt-tttcttgttccttgttcttgagatattaatgcagtgacacttctgatgatttcacagGAGACAGAGAAGGTGGCCTTGGCTGAAACTACTGGTTTGGACCAGAAACAAATTAATAATTGGTTCATAAACCAAAGGAAAAGACACTGGAAACCTTCTG
upper sequence: AT4G08150.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ10744 (Selaginella moellendorffii), 3'ss of exon 5
tctagaatcatttaaaaataattttcgattatctctagcattgctttttat-acattgattactacataaatgaagatggttggtttgagttgtgtggcagGAGTCAGAGAAGGTAGCGTTGGCGGAATCAACGGGGTTAGATCAGAAACAAATCAACAATTGGTTCATAAACCAAAGAAAGCGTCACTGGAAACCATCTG
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------------------------------------------gtatgttgtgatagttttcattgaatttatattcttagttg-tttggctggttt--cagGAACAGGAGAAAGCTAACCTCGCAACTGATACTGGACTCGACCAGAAGCAAATTAACAATTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAGMapped 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|116376083|gb|EG418675.1|EG418675EST: AGAAGCTTCTCACGTGGTGGGAGTTGCATTACAAGTGGCCATATCCTTCT GAGTCAGAGAAGGTAGCG
genomic: AGAAGCTTCTCACGTGGTGGGAGTTGCATTACAAGTGGCCATATCCTTCTgtacgtataa ... tgtgtggcagGAGTCAGAGAAGGTAGCG
EST:
gi|124788621|gb|EH878300.1|EH878300EST: GAAGCTTCTCACGTGGTGGGAGTTGCATTACAAGTGGCCAATATCCTTCT GAGTCAGAGAAGGTAGC
genomic: GAAGCTTCTCACGTGGTGGGAGTTGCATTACAAGTGGCCA-TATCCTTCTgtacgtataa ... tgtgtggcagGAGTCAGAGAAGGTAGC
EST:
gi|124994103|gb|EL066372.1|EL066372EST: ACAAGTGGCCATATCCTTCT GAGTCAGAGAAGGTAGCGTTGGCGGAAT
genomic: ACAAGTGGCCATATCCTTCTgtacgtataa ... tgtgtggcagGAGTCAGAGAAGGTAGCGTTGGCGGAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttatacattgattactacataaatgaagatggttggtttgagttgtgtggcagGAGTCAGAGAAGGTAGCGTTGGCGGAATCAACGGGGTTAGATCAGAAACAAATCAACAATTGGTTCATAAACCAAAGAAAGCGTCACTGGAAACCATCTG
cattgat putative branch site (score: 4)
attactacataaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctagaatcatttaaaaataattttcgattatctctagcattgctttttatacattgattactacataaatgaagatggttggtttgagttgtgtggcagGAGTCAGAGAAGGTAGCGTTGGCGGAATCAACGGGGTTAGATCAGAAACAAATCAACAATTGGTTCATAAACCAAAGAAAGCGTCACTGGAAACCATCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- -agaatca
- - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtttga