Sequence
atgc intronic sequence ATGC exonic sequencegtaaatcatcttttctaaactttatgtctctttgaccttgttgtatgatttatttatataatatgataatggatatttgaagGCGGAGAATTATCAGAAAGAGATTGAAGACATGAAGAACATGACTAGACAAGAATATGTTGCACATTTGAGAAGGAAGAGCAGTGGTTTCTCTAGGGGTG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G37750.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G17010.1 (Glycine max), 3'ss of exon 5
--------------------------------------------gtaaatcatcttttctaaacttta--tgtctctttgaccttgttgtatgatttatttatataatatgataatggatatttgaagGCGGAGAATTATCAGAAAGAGATTGAAGACATGAAGAACATGACTAGACAAGAATATGTTGCACATTTGAGAAGGAAGAGCAGTGGTTTCTCTAGGGGTG
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gtaataactaataacttatttctcttttctcttccatgtttccactgactcaagtttcagtaactgtgactaaaataataatcttatggcattttttttct-tcttttccattctcttctaataaaagTTGGAAAATTATCAAAATGAACTTGAGGAAATGAAGAACATGACTAGACAAGAGTATGTTGCTCATTTGAGAAG--------------------------
upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G22970.1 (Glycine max), 3'ss of exon 7
------------gtaaatcatcttttctaaactttatgtctc---tttgaccttgttgtatgatttatttatataatatgataatggatattt-------------------------gaagGCGGAGAATTATCAGAAAGAGATTGAAGACATGAAGAACATGACTAGACAAGAATATGTTGCACATTTGAGAAGGAAGAGCAGTGGTTTCTCTAGGGGTG
|| || |||||| | | |||| || | | | ||| ||| | | | | |||||| | || || |||| || ||| |||||||| || || |||| || ||||||||||||||||||||||| |||||||| |||||||||||
gtaaaactaataatatatt-tcttttttctcttccatgtttccactctcaagttgcagtaactgtgactaaaataataatctcattgacatttttttcttttccattctcttctaataacagTTGGAAAATTATCAAAATGAACTTGAGGAAATGAAGAACATGACTAGACAAGAGTATGTTGCTCATTTGAGAAG--------------------------
upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G40380.1 (Glycine max), 3'ss of exon 4
gtaa--atcatcttttctaaactttatgt-ctctttgaccttgt--------tgtatgatttatttatata----atatgataatggatatttga-agGCGGAGAATTATCAGAAAGAGATTGAAGACATGAAGAACATGACTAGACAAGAATATGTTGCACATTTGAGAAGGAAGAGCAGTGGTTTCTCTAGGGGTG
|||| || | || | | | ||||| | ||| ||| || | | |||||| | | || || | ||| ||| | || ||| |||||||| || || |||| || |||||||||||||| ||||||||||||||||| ||||| ||||
gtaatgattactttctttctaatttatcttctcaatgagtccgtattcagcttccaggatttaataacgtaactaatgcaagtatgaccttttaacagTTGGAAAATTATCAAAACGAACTTGAGGAAATGAAGAACATGACGAGACAAGAATATGTTGCTCATTTACGAAG--------------------------
upper sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G04910.1 (Glycine max), 3'ss of exon 5
----------gtaaatcatcttttctaaactttatgtctctttgaccttgttgtatgatttatttatataatatga-----taatggatatttga---------agGCGGAGAATTATCAGAAAGAGATTGAAGACATGAAGAACATGACTAGACAAGAATATGTTGCACATTTGAGAAGGAAGAGCAGTGGTTTCTCTAGGGGTG
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gtaatgattactttttttttttcttctcattttttttctgattgggtctgtattcagcttccaggatttaataacagtaactaatgcatgtatgatctattaacagTTGGAAAATTATCAAAACGAACTTGAGGAAATGAAGAACATGACGAGACAAGAATATGTAGCTCATTTACGAAG--------------------------Mapped 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|124912818|gb|EH986805.1|EH986805EST: CACACCAATTTCTCT GCGGAGAATTATCAGAAAGAGATTGAAGACATGAAGAACATGA
genomic: CACACCAATTTCTCTgtaaatcatc ... atatttgaagGCGGAGAATTATCAGAAAGAGATTGAAGACATGAAGAACATGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctctttgaccttgttgtatgatttatttatataatatgataatggatatttgaagGCGGAGAATTATCAGAAAGAGATTGAAGACATGAAGAACATGACTAGACAAGAATATGTTGCACATTTGAGAAGGAAGAGCAGTGGTTTCTCTAGGGGTG
ctttgac putative branch site (score: 4)
ttgtatgatttattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatcatcttttctaaactttatgtctctttgaccttgttgtatgatttatttatataatatgataatggatatttgaagGCGGAGAATTATCAGAAAGAGATTGAAGACATGAAGAACATGACTAGACAAGAATATGTTGCACATTTGAGAAGGAAGAGCAGTGGTTTCTCTAGGGGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG