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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgttataatagacggtccttaagtcattatgtacaacgaaatctgtaattactagttagtggaagtctgaaagatctaatatgcttgtacttgtacagGCTGGGACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCATCCTAG

Basic information

species Glycine max
transcript GLYMA14G39890.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G39890.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os04g47380.1 (Oryza sativa), 3'ss of exon 13
----aatgttataatagacggtccttaagtcattatgtacaacgaaatctgtaattactagttagtggaagtctgaaagatctaat--atgcttgtacttgtacagGCTGGGACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCATCCTAG
    |||| | |  |  |     | |||| || |   | |||    || | || |   ||||| |      ||     | | ||||  |   | ||     ||||||||||||| ||||| ||||| ||||| || || |||||||||||||| || || ||
cttaaatgcttttgtgaatccgtcataaggcaattcat-caaaagcatttatattctgtagtttgc-----tccctccggtttaatcaaccttggtgtccatacagGCTGGGACATACATAAAGGAGTTTGTGCACGGAGATCTTGGACGCACACACCCAAG

upper sequence: GLYMA14G39890.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G101383_T02 (Zea mays), 3'ss of exon 12
-----aatgttataatagacggtccttaagtcattatgtacaacgaaatctgtaattactagttagtggaagtctgaaagatctaatatgcttgtacttgtacagGCTGGGACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCATCCTAG
        | ||| | ||  | | | |||    | | |   ||  |   |  || ||    | |  ||    |   |   ||| | |  |  | |  ||  | ||||||| || ||||||||||||||||| ||||| |||||||||||||| ||||| ||
gtttcgtagatatca-aggtgatgcataaaaagtaaggcctaattatgcccttagttttctggt--tgctctttctagtaatccactg-gtatatgttta-atagGCTGGAACATACATCAAGGAATTTGTGCATGGTGATCTTGGACGCACGCATCCCAG

upper sequence: GLYMA14G39890.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv18s0001g00500.t01 (Vitis vinifera), 3'ss of exon 13
------------------------------------------------------------aatgttataatagacggtcc--ttaagtcattatg--tacaacga--aatctgtaattactagttagtggaagtctgaaagatctaata-tgcttgtacttgtacagGCTGGGACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCATCCTAG
                                                             ||| |  |  | |    |    ||    | | ||  | | | |   |  || | ||    | ||  ||||| |   |||   |||||  || |  |     | |||||||| || || ||||||||||||||||| || |||||||||||||||||||||||
gtacttaattttgcatctgctttatcaaatatttgctggatactgactattttcgagttttatgcttaaggaaagaacctggctagactactttgagtcctatggttagccttttatgttcactttttggaattagtaaaatactaatggtgatattcaaaatgcagGCTGGAACATATATCAAGGAATTTGTTCACGGTGATCTTGGACGCACCCATCCTAG

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|51342518|gb|CO983503.1|CO983503
EST:     AGACAATTGCGGGAAGTTCCCAATATTTTCTTTTGCACCTATGTACACAG                         GCTGGGACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCAT
genomic: AGACAATTGCGGGAAGTTCCCAATATTTTCTTTTGCACCTATGTACACAGgtattgtctt ... acttgtacagGCTGGGACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCAT
EST: gi|58017398|gb|CX704140.1|CX704140
EST:     AGACAATTGCGGGAAGTTCCCAATATTTTCTTTTGCACCTATGTACACAG                         GCTGGGACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCAT
genomic: AGACAATTGCGGGAAGTTCCCAATATTTTCTTTTGCACCTATGTACACAGgtattgtctt ... acttgtacagGCTGGGACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCAT
EST: gi|208221094|gb|GE020764.1|GE020764
EST:     AGACAATTGCGGGAAGTTCCCAATATTTTCTTTTGCACCTATGTACACAG                         GCTGGGACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCAT
genomic: AGACAATTGCGGGAAGTTCCCAATATTTTCTTTTGCACCTATGTACACAGgtattgtctt ... acttgtacagGCTGGGACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCAT
EST: gi|58017203|gb|CX703945.1|CX703945
EST:     AGACAATTGCGGGAAGTTCCCAATATTTTCTTTTGCACCTATGTACACAG                         GCTGGGACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCAT
genomic: AGACAATTGCGGGAAGTTCCCAATATTTTCTTTTGCACCTATGTACACAGgtattgtctt ... acttgtacagGCTGGGACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCAT
EST: gi|163922935|gb|EH039556.1|EH039556
EST:     CGGGAAGTTCCCAATATTTTCTTTTGCACCTATGTACACAG                         GCTGGGACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCAT
genomic: CGGGAAGTTCCCAATATTTTCTTTTGCACCTATGTACACAGgtattgtctt ... acttgtacagGCTGGGACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCAT
EST: gi|51342063|gb|CO983330.1|CO983330
EST:     AGACAATTGCGGGAAGTTCCCAATATTTTCTTTTGCACCTATGTACACAG                         GCTGGGACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCAT
genomic: AGACAATTGCGGGAAGTTCCCAATATTTTCTTTTGCACCTATGTACACAGgtattgtctt ... acttgtacagGCTGGGACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaattactagttagtggaagtctgaaagatctaatatgcttgtacttgtacagGCTGGGACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCATCCTAG
                              atctaat  putative branch site (score: 3)
                              atctaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgttataatagacggtccttaagtcattatgtacaacgaaatctgtaattactagttagtggaagtctgaaagatctaatatgcttgtacttgtacagGCTGGGACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCATCCTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA