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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgttcttaatttgtgtttgtgtatatttgattataggtctacttcattgtgaattaaatttcaaaatagtttttttttcccctcttcatttttaaattcctatatacagGCGGATAGAGACCCCATGCCTCTTCACCGTGCTGCAAAGTTGCTCATTAATTCTCAGTTGGAAGAGGGTGATTGGCCCCAACAG

Basic information

species Glycine max
transcript GLYMA07G00330.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00330.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv09s0054g01230.t01 (Vitis vinifera), 3'ss of exon 16
gttcgttcttaatttgtgtttgtgtatatttgattataggtctacttcattgtgaat-taaatttcaaaatagtttttttttcc---cctcttcatttttaaattcctatata-cagGCGGATAGAGACCCCATGCCTCTTCACCGTGCTGCAAAGTTGCTCATTAATTCTCAGTTGGAAGAGGGTGATTGGCCCCAACAG
        ||| ||| |     |  ||   | | || || |  ||||  |  |  |  | | ||||| ||||    || |  ||   | |||   | |     ||||| | || ||||| || |||||||| |  ||||||||| | |||||||||||| | |||||||| ||  ||||||| |||||||  |||||||||
-------gttattttatacagtttcat-catcacta-agcttaacttggtcatctacattattttcacaatatggcttctccccaaacatctgagtctaacctttcctttctaacagGCTGAGAGAGACCCAACACCTCTTCACAGGGCTGCAAAGTTGTTGATTAATTCCCAAATGGAAGATGGTGATTTTCCCCAACAG
















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|58014627|gb|CX701369.1|CX701369
EST:     ATGTTGTACATACAGCATGGGCTCTTATGGGACTAATTCATGCTGGACAG                         GCGGATAGAGACCCCATGCCTCTTCACCGTGCTGCAAAGTTGCTCATTAAT
genomic: ATGTTGTACATACAGCATGGGCTCTTATGGGACTAATTCATGCTGGACAGgttcgttctt ... ctatatacagGCGGATAGAGACCCCATGCCTCTTCACCGTGCTGCAAAGTTGCTCATTAAT
EST: gi|214008349|gb|DB986291.1|DB986291
EST:     ATGTTGTACATACAGCATGGGCTCTTATGGGACTAATTCATGCTGGACAG                         GCGGATAGAGACCCCATGCCTCTTCACCGTGCTGCAAAGTTGCTCATTAAT
genomic: ATGTTGTACATACAGCATGGGCTCTTATGGGACTAATTCATGCTGGACAGgttcgttctt ... ctatatacagGCGGATAGAGACCCCATGCCTCTTCACCGTGCTGCAAAGTTGCTCATTAAT
EST: gi|9987711|gb|BE661819.1|BE661819
EST:     ATGTTGTACATACAGCATGGGCTCTTATGGGACTAATTCATGCTGGACAG                         GCGGATAGAGACCCCATGCCTCTTCACCGTGCTGCAAAGTTGCTCATTAAT
genomic: ATGTTGTACATACAGCATGGGCTCTTATGGGACTAATTCATGCTGGACAGgttcgttctt ... ctatatacagGCGGATAGAGACCCCATGCCTCTTCACCGTGCTGCAAAGTTGCTCATTAAT
EST: gi|6914837|gb|AW396367.1|AW396367
EST:     ATGTTGTACATACAGCATGGGCTCTTATGGGACTAATTCATGCTGGACAG                         GCGGATAGAGACCCCATGCCTCTTCACCGTGCTGCAAAGTTGCTCATTAAT
genomic: ATGTTGTACATACAGCATGGGCTCTTATGGGACTAATTCATGCTGGACAGgttcgttctt ... ctatatacagGCGGATAGAGACCCCATGCCTCTTCACCGTGCTGCAAAGTTGCTCATTAAT
EST: gi|4395927|gb|AI494924.1|AI494924
EST:     ATGTTGTACATACAGCATGGGCTCTTATGGGACTAATTCATGCTGGACAG                         GCGGATAGAGACCCCATGCCTCTTCACCGTGCTGCAAAGTTGCTCATTAAT
genomic: ATGTTGTACATACAGCATGGGCTCTTATGGGACTAATTCATGCTGGACAGgttcgttctt ... ctatatacagGCGGATAGAGACCCCATGCCTCTTCACCGTGCTGCAAAGTTGCTCATTAAT
EST: gi|208148712|gb|GD951210.1|GD951210
EST:     ATGTTGTACATACAGCATGGGCTCTTATGGGACTAATTCATGCTGGACAG                         GCGGATAGAGACCCCATGCCTCTTCACCGTGCTGCAAAGTTGCTCATTAAT
genomic: ATGTTGTACATACAGCATGGGCTCTTATGGGACTAATTCATGCTGGACAGgttcgttctt ... ctatatacagGCGGATAGAGACCCCATGCCTCTTCACCGTGCTGCAAAGTTGCTCATTAAT
EST: gi|10844420|gb|BF067711.1|BF067711
EST:     ATGTTGTACATACAGCATGGGCTCTTATGGGACTAATTCATGCTGGACAG                         GCGGATAGAGACCCCATGCCTCTTCACCGTGCTGCAAAGTTGCTCATTAAT
genomic: ATGTTGTACATACAGCATGGGCTCTTATGGGACTAATTCATGCTGGACAGgttcgttctt ... ctatatacagGCGGATAGAGACCCCATGCCTCTTCACCGTGCTGCAAAGTTGCTCATTAAT
EST: gi|209699719|gb|BW652091.1|BW652091
EST:     ATGTTGTACATACAGCATGGGCTCTTATGGGACTAATTCATGCTGGACAG                         GCGGATAGAGACCCCATGCCTCTTCACCGTGCTGCAAAGTTGCTCATTAAT
genomic: ATGTTGTACATACAGCATGGGCTCTTATGGGACTAATTCATGCTGGACAGgttcgttctt ... ctatatacagGCGGATAGAGACCCCATGCCTCTTCACCGTGCTGCAAAGTTGCTCATTAAT
EST: gi|26060234|gb|CA803148.1|CA803148
EST:     ATGTTGTACATACAGCATGGGCTCTTATGGGACTAATTCATGCTGGACAG                         GCGGATAGAGACCCCATGCCTCTTCACCGTGCTGCAAAGTTGCTCATTAAT
genomic: ATGTTGTACATACAGCATGGGCTCTTATGGGACTAATTCATGCTGGACAGgttcgttctt ... ctatatacagGCGGATAGAGACCCCATGCCTCTTCACCGTGCTGCAAAGTTGCTCATTAAT
EST: gi|209707635|gb|BW683428.1|BW683428
EST:     TCTTATGGGACTAATTCATGCTGGACAG                         GCGGATAGAGACCCCATGCCTCTTCACCGTGCTGCAAAGTGTGCTCATTAA
genomic: TCTTATGGGACTAATTCATGCTGGACAGgttcgttctt ... ctatatacagGCGGATAGAGACCCCATGCCTCTTCACCGTGCTGCAAAGT-TGCTCATTAA
EST: gi|209724228|gb|BW666593.1|BW666593
EST:     ATGTTGTACATACAGCATGGGCTCTTATGGGACTAATTCATGCTGGACAG                         GCGGATAGAGACCCCATGCCTCTTCACCGTGCTGCAAAGTTGCTCATTAAT
genomic: ATGTTGTACATACAGCATGGGCTCTTATGGGACTAATTCATGCTGGACAGgttcgttctt ... ctatatacagGCGGATAGAGACCCCATGCCTCTTCACCGTGCTGCAAAGTTGCTCATTAAT
EST: gi|213588945|gb|DB984416.1|DB984416
EST:     ATGTGGTACATACAGCATAGGCTCTTATGGGACTAATTCATGCTGGACAG                         GCGGATAGACACCCCATGCCTCTTCACCGTGCTGCAAAGTTGCTCATTAAT
genomic: ATGTTGTACATACAGCATGGGCTCTTATGGGACTAATTCATGCTGGACAGgttcgttctt ... ctatatacagGCGGATAGAGACCCCATGCCTCTTCACCGTGCTGCAAAGTTGCTCATTAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaatttcaaaatagtttttttttcccctcttcatttttaaattcctatatacagGCGGATAGAGACCCCATGCCTCTTCACCGTGCTGCAAAGTTGCTCATTAATTCTCAGTTGGAAGAGGGTGATTGGCCCCAACAG
               tttttttttcccctct  CT-rich tract
                              ttcatttttaaattcc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgttcttaatttgtgtttgtgtatatttgattataggtctacttcattgtgaattaaatttcaaaatagtttttttttcccctcttcatttttaaattcctatatacagGCGGATAGAGACCCCATGCCTCTTCACCGTGCTGCAAAGTTGCTCATTAATTCTCAGTTGGAAGAGGGTGATTGGCCCCAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG