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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtggcttaaaattgaatattccttcagattgaccatgtacatttcaaacattattatttttcatatgctccctctattgaagcttatgatttacacatggattgcagGTTATTGGTATTGATTTGTTATCTCAGTCTCTGTTGCCAGCCATAGTAGAATTAGCTGAGGATCGGCACTGGAGAGTTCGACTTGCAATCATAGAATACA

Basic information

species Glycine max
transcript GLYMA07G10000.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 8
--gtttgtggcttaaaattgaatattccttcagattgaccatgtacatttcaaacattattatttttcatatgctccctctattgaagcttatgatttacacatggattgcagGTTATTGGTATTGATTTGTTATCTCAGTCTCTGTTGCCAGCCATAGTAGAATTAGCTGAGGATCGGCACTGGAGAGTTCGACTTGCAATCATAGAATACA
         ||| || ||   || |   ||  | ||  | |   |    | | | |||  |   |   | |   | | |   |     ||| |||| |          | ||||||||||| ||||||||| | || || || ||||| || || || |||||| | || |||||| |||||||||| ||||| |||||||| || || ||||
agtcccacagctcaatataacatttcaattttgcttcccta---atgactgataaattccttggtcatagaaaattcattactgagtccttttgatct----------ttcagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAACTTGCAGAGGATAGGCACTGGAGGGTTCGGCTTGCAATAATTGAGTACA

upper sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 8
------------------------------------------------gtttgtggcttaaaattgaatattccttcagat---tgaccatgtacatttcaaacattatta--------tttttcatatgct---ccctctattgaagcttat------------gatttacacatgga--ttgcagGTTATTGGTATTGATTTGTTATCTCAGTCTCTGTTGCCAGCCATAGTAGAATTAGCTGAGGATCGGCACTGGAGAGTTCGACTTGCAATCATAGAATACA
                                                ||||  |  ||  |||  ||| ||   | || |   |  ||||    ||   | |  || |||        |  || | |  ||   |  ||| || ||  ||||            |||||     | ||  || ||||||||||| ||||| ||| ||||||| || ||| | ||||| || |||||| | || |||||| ||||||||||||| || |||||||| || || ||||
gtcagtaccattttttttgttattagatttatttgccttttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagatttttttaagttgatgtccttgaaagccttgcctttctcttcaaaattatctgatgattgctgatttttgttttgatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA

upper sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 8
-----------------------------------------------gtttgtggcttaaaa---ttgaatatt--ccttcagattgaccatgtacatttcaaacattattattttt-catatgctccctctattgaag-----------cttatgatttacacatggat--tgcagGTTATTGGTATTGATTTGTTATCTCAGTCTCTGTTGCCAGCCATAGTAGAATTAGCTGAGGATCGGCACTGGAGAGTTCGACTTGCAATCATAGAATACA
                                                ||||   |||  ||   |||  ||    |  | ||  ||      |   ||| |  || | |  | |   | |   ||||||||    ||             |  ||| ||     | |||  | ||||||||||| ||||| || ||||| ||  | ||| | |||||||| |||||| | || |||||| ||||||||||||| || |||||||| || || ||||
gtcagtaccattttttgttactggatttctttgccttttccttgccgttttggatctttgaagtcttgtttaccagctattagtatgctggaatttttttaagtcactgtcctgtaagcctggcctccctcttcaaaaaagttctgttgattggtgaattttgttttgatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA

upper sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 8
gtttgtggcttaaaattgaatattccttcagat---tgaccatgtacatttcaaacattattatttttcatatgctccctctattgaagcttatgatttacacatggattgcagGTTATTGGTATTGATTTGTTATCTCAGTCTCTGTTGCCAGCCATAGTAGAATTAGCTGAGGATCGGCACTGGAGAGTTCGACTTGCAATCATAGAATACA
           | ||| |  | ||  || | |    ||  || |    || |   ||| |||    |||||    |       ||| |  || |    |  |  |   || ||||||||||| ||||| ||||| || || || ||  |||||||||| |||||  |  |||| ||| |||||||||||||||| ||||| || || || ||||
-----------agaataggctttttttttaaacttgtgttcaagatgtttcctggcatcatt-cacttcattcaatgatgtacttgtaagttctctcctgtatttt--tttcagGTTATTGGAATTGACTTGTTGTCGCAATCACTTCTGCCAGCCATTGTAGAGCTCTCTGAAGATAGGCACTGGAGAGTTCGGCTTGCCATAATTGAGTACA

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|193520014|gb|FK474603.1|FK474603
EST:     TTCCTGATGTCAGGCTAAATATTATCAGCAAGCTTGATCAAGTGAACCAG                         GTTATTGGTATTGATTTGTTATCTCAGTCTCTGTTGCCAGCCATAGTAGAA
genomic: TTCCTGATGTCAGGCTAAATATTATCAGCAAGCTTGATCAAGTGAACCAGgtttgtggct ... tggattgcagGTTATTGGTATTGATTTGTTATCTCAGTCTCTGTTGCCAGCCATAGTAGAA
EST: gi|14258560|gb|BG881468.1|BG881468
EST:     TTCCTGATGTCAGGCTAAATATTATCAGCAAGCTTGATCAAGTGAACCAG                         GTTATTGGTATTGATTTGTTATCTCAGTCTCTGTTGCCAGCCATAGTAGAA
genomic: TTCCTGATGTCAGGCTAAATATTATCAGCAAGCTTGATCAAGTGAACCAGgtttgtggct ... tggattgcagGTTATTGGTATTGATTTGTTATCTCAGTCTCTGTTGCCAGCCATAGTAGAA
EST: gi|8285673|gb|BE023232.1|BE023232
EST:     TTCCTGATGTCAGGCTAAATATTATCAGCAAGCTTGATCAAGTGAACCAG                         GTTATTGGTATTGATTTGTTATCTCAGTCTCTGTTGCCA
genomic: TTCCTGATGTCAGGCTAAATATTATCAGCAAGCTTGATCAAGTGAACCAGgtttgtggct ... tggattgcagGTTATTGGTATTGATTTGTTATCTCAGTCTCTGTTGCCA
EST: gi|192310534|gb|FG999543.1|FG999543
EST:     TTCCTGATGTCAGGCTAAATATTATCAGCAAGCTTGATCAAGTGAACCAG                         GTTATTGGTATTGATTTGTTATCTCAGTCTCTGTTGCCAGCCATAGTAGAA
genomic: TTCCTGATGTCAGGCTAAATATTATCAGCAAGCTTGATCAAGTGAACCAGgtttgtggct ... tggattgcagGTTATTGGTATTGATTTGTTATCTCAGTCTCTGTTGCCAGCCATAGTAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatttttcatatgctccctctattgaagcttatgatttacacatggattgcagGTTATTGGTATTGATTTGTTATCTCAGTCTCTGTTGCCAGCCATAGTAGAATTAGCTGAGGATCGGCACTGGAGAGTTCGACTTGCAATCATAGAATACA
                               ttatgattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtggcttaaaattgaatattccttcagattgaccatgtacatttcaaacattattatttttcatatgctccctctattgaagcttatgatttacacatggattgcagGTTATTGGTATTGATTTGTTATCTCAGTCTCTGTTGCCAGCCATAGTAGAATTAGCTGAGGATCGGCACTGGAGAGTTCGACTTGCAATCATAGAATACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA