Sequence
atgc intronic sequence ATGC exonic sequence...gtattagggtgatgataatgagagttaagttttggtacagattgtcatatatagttatgcagtattttcttctaatatctgattgatctttcttttctagTTTGACTGAAATTCAGAATGCACGTGGCATCATGGATGTTCTTGCAGAAATGCTCAATGCCTTAGACCCTAGTAACAAAGAA
Basic information
species | Glycine max |
transcript | GLYMA17G26440.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G26440.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g17350.2 (Oryza sativa), 3'ss of exon 5
-----------------------gtattagggtgatgataatgagagttaagttttggtacagattgtcatatatagttatgcagtattttcttcta-atatctgat--tgatctttctttt----ctagTTTGACTGAAATTCAGAATGCACGTGGCATCATGGATGTTCTTGCAGAAATGCTCAATGCCTTAGACCCTAGTAACAAAGAA
||||| || | | | | ||| | | || | | | | || ||| || || | || || | ||||| || || | | || | | ||||||||||||||||| |||||||||||||||||| | || ||| | ||||| || || |||||||||| |||
gtattgcagtttttgaaattttcttattacaatggatgtgtatactactgaactttagca----tttcaaaaaagaattgaaacatatgtttccatacaaatttggtaatgatcatttttatttcaccagCCTAGCAGAAATTCAGAATGCACGAGGCATCATGGATGTTCTTTCCGAGATGTTGAATGCTTTGGATCCTAGTAACAGAGAG
upper sequence: GLYMA17G26440.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g22650.1 (Oryza sativa), 3'ss of exon 5
----gtattagggtgatgataatgagagttaagttttggtacagattgtcatatatagttatgcagtattttcttctaatatctgattgatct-ttcttttctagTTTGACTGAAATTCAGAATGCACGTGGCATCATGGATGTTCTTGCAGAAATGCTCAATGCCTTAGACCCTAGTAACAAAGAA
| | | | || ||| | | ||| || | || | | | | | || | | | ||||| | |||| || | |||||||| ||||| |||||||||||||| |||||||||||||| |||| ||| | ||||| | || ||| | |||| |||
ggccttgtcaagcaactgc--atgtaattccctctttaatattaaa-gttgccttttctaaggaaggtataaatcacattatcttgt--atctactccccaccagTTTGACAGAAATCCAGAATGCACGTGGTGTCATGGATGTTCTTTCAGAGATGTTGAATGCTATTGATCCTGGCAACAGAGAG
upper sequence: GLYMA17G26440.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G053925_T02 (Zea mays), 3'ss of exon 5
--gtattagggtgatgataatgagagttaagttttggtacagattgtcatatatagttatgcagtattttcttctaatatctgattgatctttcttttctagTTTGACTGAAATTCAGAATGCACGTGGCATCATGGATGTTCTTGCAGAAATGCTCAATGCCTTAGACCCTAGTAACAAAGAA------------------
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ttatatttatttcatgttttagatgtttgtgaacttgctgttgtcattggtttagcctatccagcatacaagtttggtaa-tgattg-cggtaatttaccagCCTTACAGAAATTCAGAACGCACGTGGCATCATGGATGTTCTTTCAGAGATGCTGGATGCTTTAGATCCAGGTAACAGAGAGGTACTTTCCTGATGCACC
upper sequence: GLYMA17G26440.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G053925_T01 (Zea mays), 3'ss of exon 5
--gtattagggtgatgataatgagagttaagttttggtacagattgtcatatatagttatgcagtattttcttctaatatctgattgatctttcttttctagTTTGACTGAAATTCAGAATGCACGTGGCATCATGGATGTTCTTGCAGAAATGCTCAATGCCTTAGACCCTAGTAACAAAGAA
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ttatatttatttcatgttttagatgtttgtgaacttgctgttgtcattggtttagcctatccagcatacaagtttggtaa-tgattg-cggtaatttaccagCCTTACAGAAATTCAGAACGCACGTGGCATCATGGATGTTCTTTCAGAGATGCTGGATGCTTTAGATCCAGGTAACAGAGAG
upper sequence: GLYMA17G26440.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G077844_T01 (Zea mays), 3'ss of exon 5
gtattagggtgatgataatgagagttaagt---tttggtacagattgtcatatatagttatgcagtattttcttctaatatctgattgatctttcttttctagTTTGACTGAAATTCAGAATGCACGTGGCATCATGGATGTTCTTGCAGAAATGCTCAATGCCTTAGACCCTAGTAACAAAGAA
|| || | || || | | ||| | | | || | | | || | | || || | ||| | |||| ||| || || | || ||||| |||||||||||||||||||| |||||||||||||| |||| ||| | ||||| | || ||| |||||| |||
gttataatttaatcattgttatgattagctgtgtcttgtttatttgatgattttccttcataaaggaagttcc-caaataat--gttgcctttctattgccagCTTGACAGAAATTCAGAATGCACGTGGGGTCATGGATGTTCTTTCAGAGATGTTAAATGCTATCGATCCTGGTAACAGAGAG
upper sequence: GLYMA17G26440.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 5
gtattagggtgatgataatgagagttaagttttggtacagattgtca--tatatagttatgcagtattttcttctaatatctgattgatct-ttcttttctagTTTGACTGAAATTCAGAATGCACGTGGCATCATGGATGTTCTTGCAGAAATGCTCAATGCCTTAGACCCTAGTAACAAAGAA
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---taaaatctgtctctctggttaacatcttttattgcatggtttcgatctttttgcaagttattatgcatgtcttgtttttaatttgtatattccttcctagTTTGACAGAAATTCAGAATGCACGAGGTATTATGGATGTCCTTGCAGAAATGCTGAGTGCATTAGATCCAGGAAACAAAGAGMapped 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|17021949|gb|BM092983.1|BM092983EST: GACCAGGACGCAGCTCAGTCCTCTGCAGAGTCTGAGTTTCCAACACTCAA TTTGACTGAAATTCAGAATGCACGTGGCATCATGGATGTTCTTGCAGAAAT
genomic: GACCAGGACGCAGCTCAGTCCTCTGCAGAGTCTGAGTTTCCAACACTCAAgtatggatct ... tcttttctagTTTGACTGAAATTCAGAATGCACGTGGCATCATGGATGTTCTTGCAGAAAT
EST:
gi|16105990|gb|BI893730.1|BI893730EST: GACTTTTACGCAGCTCAGTCCTCTGCAGAGTCTGAGTTTCCAACACTCAA TTTGACTGAAATTCAGAATGCACGTGGCATCATGGATGTTCTTGCAGAAAT
genomic: GACCAGGACGCAGCTCAGTCCTCTGCAGAGTCTGAGTTTCCAACACTCAAgtatggatct ... tcttttctagTTTGACTGAAATTCAGAATGCACGTGGCATCATGGATGTTCTTGCAGAAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catatatagttatgcagtattttcttctaatatctgattgatctttcttttctagTTTGACTGAAATTCAGAATGCACGTGGCATCATGGATGTTCTTGCAGAAATGCTCAATGCCTTAGACCCTAGTAACAAAGAA
ttgatctttcttttct CT-rich tract
tattttcttctaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattagggtgatgataatgagagttaagttttggtacagattgtcatatatagttatgcagtattttcttctaatatctgattgatctttcttttctagTTTGACTGAAATTCAGAATGCACGTGGCATCATGGATGTTCTTGCAGAAATGCTCAATGCCTTAGACCCTAGTAACAAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - -ggtgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - -gttatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgattg