Sequence
atgc intronic sequence ATGC exonic sequence...atttgactttgtaactaattttctttaattggttttcatcattgtttttgttttatcagttttaatttattttttgcctcttctttttaaaatataacagTCAATTGAATTCAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGGCAAGAGTTTAGTGGGTATACTACACAA
Basic information
species | Glycine max |
transcript | GLYMA10G02040.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G02040.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 5
atttgactttgtaactaattttctttaattggttttcatcattgtttttgttt-tatcagttttaatttattttttgcctcttctttttaaaatataacagTCAATTGAATTCAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGGCAAGAGTTTAGTGGGTATACTACACAA
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attcttttcctgattgaagttcgtattaataattaggtgcttcataccaatttgtacatgctaatgctaatgttttggatttgctaacgtgactgtg-cagACTATTGAGTTTAAAGACATAATTAAAATTGGACGTACACATACCCAAGATGCCACCCCATTGACTCTTGGCCAAGAATTCAGTGGCTACACTACACAG
upper sequence: GLYMA10G02040.2 (Glycine max), 3'ss of exon 5
lower sequence: AT5G50950.3 (Arabidopsis thaliana), 3'ss of exon 4
atttgactttgtaactaattttctttaattggttttcatcattgtttttgttttatcagttttaatttattt--tttgcctcttctttttaaaatata-acagTCAATTGAATTCAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGGCAAGAGTTTAGTGGGTATACTACACAA
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ctttgac---gtcattttgttatttaatccaaaattcatatactctattttctctgcagtcttaacattttaaatttatctcatcttattcggttttggacagTCCTTCGAGTTTAAAGATATAGTGAAAATCGGAAGAACTCATACTCAAGATGCTACACCTTTGACATTAGGACAAGAATTTGGTGGCTATGCTACTCAA
upper sequence: GLYMA10G02040.2 (Glycine max), 3'ss of exon 5
lower sequence: AT2G47510.2 (Arabidopsis thaliana), 3'ss of exon 6
--atttgactttgtaactaattttctttaattggtttt---catcattgtttttgttttatcagttttaatttattttttgcctcttctttttaaaatataacagTCAATTGAATTCAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGGCAAGAGTTTAGTGGGTATACTACACAA
| ||| | | || | | | ||| || | | || || | | | | | | | ||||| ||| || ||| || | | ||||| | || |||||||||||||| || |||||| | ||||| ||||||||||| ||||||||||| || || ||||| ||| |||| ||| |||| |||
tttctagacctcttcacattcctattgcatttgcacttgggctttatggtctatctgctctgaatcctaattc-tttccaaacttaccttgtt----tctggcagTCCTTCGAGTTCAAAGATATTGTGAAAATTGGAAGAACTCACACTCAAGATGCTACACCTTTGACACTAGGACAAGAATTTGGTGGCTATGCTACTCAA
upper sequence: GLYMA10G02040.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 6
atttgactttgtaactaattttctttaattggttttcatcattgtttttgttttatcagttttaatttattttttgcctcttctttttaaaatataacagTCAATTGAATTCAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGGCAAGAGTTTAGTGGGTATACTACACAA
| || ||||| |||| | |||| | | | || | | | | || | | | | | | | ||| | | ||||| ||||| |||||||||||| | || ||||| || ||||| |||||||||||||| ||||||||| | || |||||||||||||||||| |||||||
ggcagcctatgtaatatatttaatataatgaggactactaggtgacacaatataaaaatcattcttgcctctatgactttgcttattttgttttttccagTCTATTGAGTTCAAAGATATTATTAAAATTGGGCGTACTCACACTCAAGATGCAACGCCTTTGACTTTGGGCCAAGAGTTTAGTGGGTATTATACACAA
upper sequence: GLYMA10G02040.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S49_154V6.1 (Physcomitrella patens), 3'ss of exon 5
-atttgactttgtaactaattttctttaattggttttcatcattgtttttgttttatcagttttaat-ttattttttgcctcttctttttaaaatataacagTCAATTGAATTCAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGGCAAGAGTTTAGTGGGTATACTACACAA
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tgtttctttccaaggtggatatgcatc--ttcaagttcaatattgatttgtctgaatcttgcgtaatattggctgacggtttgatattttggtttttggcagCAAAATGATTTTAGCGACATTGTTAAGATTGGTCGCACTCATACTCAAGATGCTGTTCCACTCACCCTCGGACAAGTGTTTAGTGCATACTGCACACAGMapped 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|207685655|gb|GD667713.1|GD667713EST: CAAGACTAATTCCCAGCTTGAAAACCTTACACGGTACACTAAACTCAAAG TCAATTGAATT
genomic: CAAGACTAATTCCCAGCTTGAAAACCTTACACGGTACACTAAACTCAAAGgtttgacaag ... aatataacagTCAATTGAATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgttttatcagttttaatttattttttgcctcttctttttaaaatataacagTCAATTGAATTCAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGGCAAGAGTTTAGTGGGTATACTACACAA
ttttaat putative branch site (score: 3)
ttttaatttatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttgactttgtaactaattttctttaattggttttcatcattgtttttgttttatcagttttaatttattttttgcctcttctttttaaaatataacagTCAATTGAATTCAAAGATATTGTCAAGATTGGACGCACTCATACTCAAGATGCAACACCTTTGACTCTTGGGCAAGAGTTTAGTGGGTATACTACACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - gactttg