Sequence
atgc intronic sequence ATGC exonic sequence...taatttgtttggcatatacatgagagaaaaaattacctttcataaatatacaacttttcctgtttccttaactattgtttgttcaatttggattatacagGAGTAAAAATATGAAAACTCGTGTGATTGGGTGCCCTAAAACCATTGATGGTGATTTGAAATGCAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCA
Basic information
species | Glycine max |
transcript | GLYMA17G01360.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 5
taatttgtttggcatatacatgagagaaaaaattacctttcataaatata----caacttttcctgtttccttaactattgtttgttcaat-ttggattatacagGAGTAAAAATATGAAAACTCGTGTGATTGGGTGCCCTAAAACCATTGATGGTGATTTGAAATGCAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCA
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--aattctgcaacataga---gaatctagatattattctcgatagttttattggcaatattaactatatgcttgttgacaagtgagtgattgtttaactttgtagGGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGGAGATCTGAAATGCAAGGAGGTTCCAACAAGCTTTGGGTTTGACACTGCT
upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 5
----------------------taatttgtttggcatatacatgagagaaaaaattacctttcataaatatacaacttttcctgtttcctta----------actattgtttgttcaatttgga------ttatacagGAGTAAAAATATGAAAACTCGTGTGATTGGGTGCCCTAAAACCATTGATGGTGATTTGAAATGCAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCA
| | | || ||| ||| | || || || || | | | |||| ||| || | | | ||| | ||||| || | | ||| | || |||||||| ||||| ||||| ||||| || || || ||||| ||| ||||||| || || ||||| ||||| ||||| |||||||||||
gttggctgctaacgctgtgttttgacct-ttcaatataaggctgattgtgaatataacattgcgttggttgtttcttttttctgcttattcacaagcaaatcaaaattatgatttcaaattatgaacttgctccatagGTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGGGGATCTGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCT
upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 5
------------------------------taatttgtttggcatatacatgagaga---------aaaaattacctttcataaatatacaacttttcctgtttccttaactattgtttgttcaatttggattatacagGAGTAAAAATATGAAAACTCGTGTGATTGGGTGCCCTAAAACCATTGATGGTGATTTGAAATGCAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCA
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gtaaaccttgcagttgaatctgttatgttgaaacttatttatcttaggcgaaagtagttgttcttgaagatccatgtgaccagaatctttaatatttgctgattcagcatttgacttattatctacttgtataat-tagGAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCCCAAGACCATTGATGGTGATTTGAAATGCAAAGAGGTTCCTACTAGTTTTGGGTTTGATACAGCT
upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 5
taatttgtttggcatatacatgagagaaaaaattacctttcataaatatacaacttttcctgtttccttaactattgtttg--ttcaatttggattatacagGAGTAAAAATATGAAAACTCGTGTGATTGGGTGCCCTAAAACCATTGATGGTGATTTGAAATGCAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCA
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---------------gtaattttttgaaattgtttaagattaatgagactcacttctctctgttttgtgttttaatgtttggtttcctattcggtttt-cagAGCTAAAAACATGAAAACTCTGGTTATTGGATGCCCTAAGACAATCGATGGTGATTTAAAGAGCAAAGAAGTCCCCACGAGTTTCGGGTTTGATACTGCT
upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 5
--------taatttgtttggcatata--catgagagaaaaaattacctttcataaatatacaacttttcctgtttccttaactattgtttgttcaatttggattatacagGAGTAAAAATATGAAAACTCGTGTGATTGGGTGCCCTAAAACCATTGATGGTGATTTGAAATGCAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCA
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tgttaaattcagaaatctactatgtgatcatcagaataagaactgactct--ttagtaatcagtg------atttgtttaact-ttatttgatctatctg-acaaatcagGGGTAAAAATATGAAAGCTCGGGTGATTGGATGCCCAAAGACCATTGATGGTGATTTGAAATGCAAGGAGGTTCCCACAAGTTTTGGATTTGATACTGCAMapped 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|254330861|gb|GR842126.1|GR842126EST: GGAACAGGGACCCCCTCCCCCTCCCAATTTTCTATTTTTTCTGAAGTCAT GAGTAAAAATATGAAAACTCGTGTGATTGGGTGCCCTAAAACCATTGATGG
genomic: GGAACAGGGACCCCCTCCCCCTCCCAATTTTCTATTTTTTCTGAAGTCATgtatgtagta ... gattatacagGAGTAAAAATATGAAAACTCGTGTGATTGGGTGCCCTAAAACCATTGATGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatacaacttttcctgtttccttaactattgtttgttcaatttggattatacagGAGTAAAAATATGAAAACTCGTGTGATTGGGTGCCCTAAAACCATTGATGGTGATTTGAAATGCAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCA
ccttaac putative branch site (score: 3)
ttaactatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taatttgtttggcatatacatgagagaaaaaattacctttcataaatatacaacttttcctgtttccttaactattgtttgttcaatttggattatacagGAGTAAAAATATGAAAACTCGTGTGATTGGGTGCCCTAAAACCATTGATGGTGATTTGAAATGCAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - ttgtttg
- - - - - - catatac
- - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - -cctttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgt