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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacttgatatggaactgcaccgggattcttttttaaacaattggttgatggagcattatatacttgtttcctgcagGAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAG

Basic information

species Zea mays
transcript GRMZM2G058584_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g13190.1 (Oryza sativa), 3'ss of exon 6
--------------------------gtacacttgatatggaactgcaccgggattcttttttaaac--aattggttgatggagcattatatacttgtttcctgcagGAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAG
                           | |  ||  |  | |  ||    |    | ||| | |     ||||  |||     |  |  |   |||||   | ||||||||||||||||||||| || |||||||||||||||||  |||||||||||||||||||||||
gtacaattttattggatgcaggattgctgctatttctgagaagttgatatgtttgtgtttctaatgttgaattatttggaatcggttgttgctcttgtcctccgcagGAGGTTCTTTACTGTGCTAAAAAAGCTGGTGTGACACATGTATTGAAAGCTGGAGGAGCTCAG

upper sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA15G13910.2 (Glycine max), 3'ss of exon 6
gtacacttgatatggaactgcaccgggattcttttttaaacaattggttgatggagcattatatacttgtttcctgcagGAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAG
          |||  | ||     |        || ||  ||    |||| |   |   |    | |  ||||||||||||||| || || |||||||| || ||||| ||||| |||||  | |||||||||||||| |||
---------gtatttatctattttgtatgaaaattatagtcatgatgttgttcttgttctgaccaatgctttcctgcagGAGGTACTGTATTGTGCAAAAAAGGCTGGGGTGACTCACATTCTCAAAGCTGGAGGAGCACAG

upper sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA09G02960.1 (Glycine max), 3'ss of exon 6
gtacacttgatatggaactgcaccgggattcttttttaaacaattggttgatggagcattatatacttgtttcctgcagGAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAG
    | || || |     ||       ||| |  |    |  ||  |||| |   |   |    | |  ||||||||||||||| || || ||||||||||| ||||| ||||| |||||  | |||||||||||||| |||
--gtattt-atctatttttgtttgaaaattatagtc---atgat--gttgttcttgttctgagcaatgttttcctgcagGAGGTACTGTATTGTGCAAAGAAGGCTGGGGTGACTCACATTCTCAAAGCTGGAGGAGCACAG

upper sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 8
lower sequence: PP1S233_40V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------------------------------gtacacttg-atatggaactgcaccgggattcttttttaaacaattggttga----tggagcattatatacttg-----tttcctg-cagGAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAG
                                                              |   || | | |||    |    | | |  ||||| ||       || | |    |  |   | || ||   |     | | ||  ||||| ||  | ||||||||||||||  | |||||||| ||||| ||||||||||| |||||||||
gtaagctttatatccctggaggcttgacaagtgcacgctttgcgccataaccagatggaggctgtgctgggacatgcttttttttctgtaggcttttctagtttgcaggataaaattttaaaagtgatctaacaggagcatctgctatcagGAAGTATTGTACTGTGCAAAGAAGTCGGGTGTGACCCACATTTTGAAAGCTGGTGGAGCTCAG

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|89758985|gb|DY687956.1|DY687956
EST:     AAACTATTGTTCTTGCCACACCACCTAGCCGTGATGGTAGCATATGCAAG                         GAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCT
genomic: AAACTATTGTTCTTGCCACACCACCTAGCCGTGATGGTAGCATATGCAAGgtacacttga ... tttcctgcagGAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCT
EST: gi|8516559|gb|BE123284.1|BE123284
EST:     ATTGTTCTTGCCACACCACCTA-CCGTGATGGCAGCATATGCAAG                         GAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCT
genomic: ATTGTTCTTGCCACACCACCTAGCCGTGATGGTAGCATATGCAAGgtacacttga ... tttcctgcagGAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCT
EST: gi|21331772|gb|BQ487153.1|BQ487153
EST:     AACTA-TGTTCTTGCCACACCACCTAGCCG-GATGGCAGCATATGCAAG                         GAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCT
genomic: AACTATTGTTCTTGCCACACCACCTAGCCGTGATGGTAGCATATGCAAGgtacacttga ... tttcctgcagGAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCT
EST: gi|23357617|gb|BU645266.1|BU645266
EST:     AAACTATTGTTCTTGCCACACCACCTAGCCGTGATGGCAGCATATGCAAG                         GAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCT
genomic: AAACTATTGTTCTTGCCACACCACCTAGCCGTGATGGTAGCATATGCAAGgtacacttga ... tttcctgcagGAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCT
EST: gi|38688105|gb|CK145136.1|CK145136
EST:     AAACTATTGTTCTTGCCACACCACCTAGCCGTGATGGTAGCATATGCAAG                         GAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCT
genomic: AAACTATTGTTCTTGCCACACCACCTAGCCGTGATGGTAGCATATGCAAGgtacacttga ... tttcctgcagGAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCT
EST: gi|76012899|gb|DT940069.1|DT940069
EST:     AAACTATTGTTCTTGCCACACCACCTAGCCGTGATGGTAGCATATGCAAG                         GAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCT
genomic: AAACTATTGTTCTTGCCACACCACCTAGCCGTGATGGTAGCATATGCAAGgtacacttga ... tttcctgcagGAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCT
EST: gi|211215840|gb|FL096753.1|FL096753
EST:     AAACTATTGTTCTTGCCACACCACCTAGCCGTGATGGCAGCATATGCAAG                         GAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCT
genomic: AAACTATTGTTCTTGCCACACCACCTAGCCGTGATGGTAGCATATGCAAGgtacacttga ... tttcctgcagGAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCT
EST: gi|211320051|gb|FL096754.1|FL096754
EST:     AAACTATTGTTCTTGCCACACCACCTAGCCGTGATGGCAGCATATGCAAG                         GAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCT
genomic: AAACTATTGTTCTTGCCACACCACCTAGCCGTGATGGTAGCATATGCAAGgtacacttga ... tttcctgcagGAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCT
EST: gi|38687960|gb|CK144991.1|CK144991
EST:     AAACTATTGTTCTTGCCACACCACCTAGCCGTGATGGTAGCATATGCAAG                         GAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCT
genomic: AAACTATTGTTCTTGCCACACCACCTAGCCGTGATGGTAGCATATGCAAGgtacacttga ... tttcctgcagGAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggattcttttttaaacaattggttgatggagcattatatacttgtttcctgcagGAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAG
                     ggttgat  putative branch site (score: 5)
                                         cttgtttcct  putative PPT
     tcttttttaaacaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacttgatatggaactgcaccgggattcttttttaaacaattggttgatggagcattatatacttgtttcctgcagGAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA