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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgggcgatagagtaagtatttgctgtattcaactcaaaaaattgatagtgacagtgtatttactgaggctcctttttatgttttctttcccatgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACACAGGAAATGCTTCTAAGTTATAACAATGGAGTATGAAAGATGGACCAGGG

Basic information

species Glycine max
transcript GLYMA03G30110.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G30110.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0007g06520.t01 (Vitis vinifera), 3'ss of exon 3
---------------------------------------ttgggcgatagagtaagtatttgctgtattcaactcaaaa----------aattgata-gtgacagtgtatttactgaggctcctttttatgttttctttcccatg--tgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACACAGGAAATGCTTCTAAGTTATAACAATGGAGTATGAAAGATGGACCAGGG
                                        |   |  | || | | | |     ||| ||| ||    |            ||| || || | | | ||  | |       |  |||| | || |  ||    ||  || ||||||||||| | |||| |||||||||||| || || |||||||| || ||||||||||| |||||| | ||                             
gtacaccactttcttgtcttccattcatacaaaaagcacataaccattcgaatcattttcaatagtaatcaccttgggatccgatgtgtggttgctaagttaaaatataagtccatgacaacaattttgtcttgtggttgttttgattgcagATGTGGATTTCAAAGGGAGAGTATGATGAGTCAGGGCCATCAATTGTTCACAGGAAATGTTTCTAA-TCATGGA--------------------------

upper sequence: GLYMA03G30110.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------ttgggcgatagagtaa-gtatttgctgtattcaactcaaaaaattgatagtgacagtgtatttactgaggctcctttttatgttttctttcccatgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACACAGGAAATGCTTCTAAGTTATAACAATGGAGTATGAAAGATGGACCAGGG-
                                       ||     ||    | | || |||| | | ||||| |       ||  | | | | ||    || |||    |   |  |  |||| |||      ||| ||||||||||||||||| | ||||| ||||| || || |||||||| || |||||||| || |||||    |   | |   | | |      |    |||   
gtaatgtatttgactcgtgtctgagttgcatttcgtgtttttttttatgtcttcatgtctttgtt-tcttcaaatgctcgcgtttgtcgaggctgtaatctttctggaatt---taatccgtttacttgttgtggtgcagATGTGGATTGCGAAGTCGGAGTACGATGAGTCAGGTCCATCAATTGTGCACAGGAAGTGTTTCTAGAGCAGTGCGACACA-TCTTTTGCTTTTTTCAGCAC
















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|7147334|gb|AW509256.1|AW509256
EST:     GTGTCTGGATTGGAGGCTCTATCTTGGCCTCCCTCAGCACCTTCCAACAG                         ATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
genomic: GTGTCTGGATTGGAGGCTCTATCTTGGCCTCCCTCAGCACCTTCCAACAGgtaaactgca ... ccatgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
EST: gi|193622119|gb|FK570475.1|FK570475
EST:     GTGTCTGGATTGGAGGCTCTATCTTGGCCTCCCTCAGCACCTTCCAACAG                         ATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
genomic: GTGTCTGGATTGGAGGCTCTATCTTGGCCTCCCTCAGCACCTTCCAACAGgtaaactgca ... ccatgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
EST: gi|7285227|gb|AW597714.1|AW597714
EST:     GTGTCTGGATTGGAGGCTCTATCTTGGCCTCCCTCAGCACCTTCCAACAG                         ATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
genomic: GTGTCTGGATTGGAGGCTCTATCTTGGCCTCCCTCAGCACCTTCCAACAGgtaaactgca ... ccatgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
EST: gi|193367246|gb|FK330336.1|FK330336
EST:     GTGTCTGGATTGGAGGCTCTATCTTGGCCTCCCTCAGCACCTTCCAACAG                         ATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
genomic: GTGTCTGGATTGGAGGCTCTATCTTGGCCTCCCTCAGCACCTTCCAACAGgtaaactgca ... ccatgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
EST: gi|18711426|gb|BM522592.1|BM522592
EST:     GTGTCTGGATTGGAGGCTCTATCTTGGCCTCCCTCAGCACCTTCCAACAG                         ATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
genomic: GTGTCTGGATTGGAGGCTCTATCTTGGCCTCCCTCAGCACCTTCCAACAGgtaaactgca ... ccatgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
EST: gi|208283062|gb|GE078976.1|GE078976
EST:     GTGTCTGGATTGGAGGCTCTATCTTGGCCTCCCTCAGCACCTTCCAACAG                         ATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
genomic: GTGTCTGGATTGGAGGCTCTATCTTGGCCTCCCTCAGCACCTTCCAACAGgtaaactgca ... ccatgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACAC
EST: gi|193368003|gb|FK333473.1|FK333473
EST:     GTGTCTGGATTGGAGGCTCTATCTTGGCCTCCCTCAGCACCTTCCAACAG                         ATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATACGTACA
genomic: GTGTCTGGATTGGAGGCTCTATCTTGGCCTCCCTCAGCACCTTCCAACAGgtaaactgca ... ccatgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAAT-CGTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagtgacagtgtatttactgaggctcctttttatgttttctttcccatgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACACAGGAAATGCTTCTAAGTTATAACAATGGAGTATGAAAGATGGACCAGGG
 aattgat  putative branch site (score: 4)
                        ctcctttttatgtttt  putative PPT
                            tttttatgttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgggcgatagagtaagtatttgctgtattcaactcaaaaaattgatagtgacagtgtatttactgaggctcctttttatgttttctttcccatgtgtagATGTGGATTGCGAAGGCAGAGTATGATGAATCTGGACCATCAATCGTACACAGGAAATGCTTCTAAGTTATAACAATGGAGTATGAAAGATGGACCAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - -tgctgta
- - - - - - - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - gatagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tactgag