Sequence
atgc intronic sequence ATGC exonic sequence...tggctttgtaactgattttcttaaaatggttttttatctttgcttttgttttattagtttttatttaaatttttgccttttcctctaaaaaaaatatcagTCAGTTGAATTTAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGACAAGAGTTTAGTGGATATACTACACAA
Basic information
species | Glycine max |
transcript | GLYMA02G01930.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G01930.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 5
--tggctttgtaactgattttcttaa-aatggttttttatctttgcttttgttttattagtttttatttaaatttttgccttttcctctaaaaaaaatat-cagTCAGTTGAATTTAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGACAAGAGTTTAGTGGATATACTACACAA
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attcttttcctgattgaagttcgtattaataattaggtgcttcataccaatttgtacatgctaatgctaatgttttggatttg----ctaacgtgactgtgcagACTATTGAGTTTAAAGACATAATTAAAATTGGACGTACACATACCCAAGATGCCACCCCATTGACTCTTGGCCAAGAATTCAGTGGCTACACTACACAG
upper sequence: GLYMA02G01930.2 (Glycine max), 3'ss of exon 5
lower sequence: AT5G50950.3 (Arabidopsis thaliana), 3'ss of exon 4
tggctttgtaactgattt--tcttaaaatggttttttatctttgcttttgttttattagtttttat-ttaaatttttgccttttcctctaaaaaaaatatcagTCAGTTGAATTTAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGACAAGAGTTTAGTGGATATACTACACAA
||||| ||| | || || || || | || || | | ||| || | || | ||| || || | | ||||| | || ||||||||||| || || || ||| | ||||||||||||||||| ||||||||||| | |||||||| ||| |||| ||| |||| |||
---ctttgacgtcattttgttatttaatccaaaattcatatactctattttctctgcagtcttaacattttaaatttatctcatcttattcggttttggacagTCCTTCGAGTTTAAAGATATAGTGAAAATCGGAAGAACTCATACTCAAGATGCTACACCTTTGACATTAGGACAAGAATTTGGTGGCTATGCTACTCAA
upper sequence: GLYMA02G01930.2 (Glycine max), 3'ss of exon 5
lower sequence: AT2G47510.2 (Arabidopsis thaliana), 3'ss of exon 6
tggctttgtaactgattttcttaaaatggttttttatctttgcttttgt--tttattagtttttatttaaatttttgccttttcctctaaaaaaaatatcagTCAGTTGAATTTAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGACAAGAGTTTAGTGGATATACTACACAA
| | | || | || || | ||| ||| | ||| | | ||| | | | | | | || | | | | | ||||| | || || ||||||||||| || |||||| | ||||| ||||||||||| ||||||||||| || |||||||| ||| |||| ||| |||| |||
--tttctagacctcttcacattcctattgcatttgcacttgggctttatggtctatctgctctgaatcctaattctttccaaacttaccttgtttctggcagTCCTTCGAGTTCAAAGATATTGTGAAAATTGGAAGAACTCACACTCAAGATGCTACACCTTTGACACTAGGACAAGAATTTGGTGGCTATGCTACTCAA
upper sequence: GLYMA02G01930.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 6
tggctttgtaactgattttcttaaaatggttttttatctttgcttttgttttattagtttt-tatttaaatttttgccttttcctctaaaaaaaatatcagTCAGTTGAATTTAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGACAAGAGTTTAGTGGATATACTACACAA
||| || | || | |||| || | | | | | ||| | | | || | | || |||| | | | | ||||| |||| || ||||||||| | || ||||| || ||||| |||||||||||||| ||||||||| | || |||||||||||||| ||| |||||||
-ggcagcctatgtaatatatttaatataatgaggactactaggtgacacaatataaaaatcattcttgcctctatgactttgcttattttgttttttccagTCTATTGAGTTCAAAGATATTATTAAAATTGGGCGTACTCACACTCAAGATGCAACGCCTTTGACTTTGGGCCAAGAGTTTAGTGGGTATTATACACAA
upper sequence: GLYMA02G01930.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S49_154V6.1 (Physcomitrella patens), 3'ss of exon 5
--tggctttgtaa--ctgattttcttaaaatggttttttatc--tttgcttttgttttat-tagtttttatttaaatttttgccttttcctctaaaaaaaatatcagTCAGTTGAATTTAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGACAAGAGTTTAGTGGATATACTACACAA
| |||| || ||| | | | ||| ||| |||| | | || || | || | | ||| |||| | | | ||| | ||| |||| || ||||| |||||||| |||||||||||||||||||| || | || || ||||||| |||||||| ||| |||||
tgtttctttccaaggtggatatgcatcttcaagttcaatattgatttgtctgaatcttgcgtaatattggctgacggtttgatattttggtttt-------tggcagCAAAATGATTTTAGCGACATTGTTAAGATTGGTCGCACTCATACTCAAGATGCTGTTCCACTCACCCTCGGACAAGTGTTTAGTGCATACTGCACACAGMapped 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|151394627|gb|EV264498.1|EV264498EST: CAAGACTGATCCCCAGCCTTAAAACGTTACACGATACTCTAAACTCAAAG TCAGTTGAATTTAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGAT
genomic: CAAGACTGATCCCCAGCCTTAAAACGTTACACGATACTCTAAACTCAAAGgtttgaattg ... aaaatatcagTCAGTTGAATTTAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttttattagtttttatttaaatttttgccttttcctctaaaaaaaatatcagTCAGTTGAATTTAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGACAAGAGTTTAGTGGATATACTACACAA
ctctaaa putative branch site (score: 3)
ttattagtttttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggctttgtaactgattttcttaaaatggttttttatctttgcttttgttttattagtttttatttaaatttttgccttttcctctaaaaaaaatatcagTCAGTTGAATTTAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGACAAGAGTTTAGTGGATATACTACACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA