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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttttttgttctttttgtcttcatctataactgtatccttttgtattgtctctgattacctcttgcatcagatgatggcgctttaattgcgttcatctgttgaaaatcggaagtggtgtcaatattcatatttttccaaactatcatcatcttttgttgatactcacaaaaagaaaattcgtttgaaaagGAGTATCTATCCATCGGCCGAGGAGTACATGATTCATGCTGAAAGGTCAAATGAGAGTTTAGTGGAAGCTTTTAAAAATATGCATGTACATGAAGAGATG

Basic information

species Zea mays
transcript GRMZM2G141587_T01
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141587_T03 (Zea mays), 3'ss of exon 22
lower sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 13
gtttttttgttctttttgtcttcatctataactgtatccttttgtattgtctctgattacctcttgcatcagatgatggcgctttaattgcgttcatctgttgaaa--atcggaagtggtgtcaatattcatatttttccaaactatcatcatcttttgttgatactcacaaaaagaaaattcgtttgaaaagGAGTATCTATCCATCGGCCGAGGAGTACATGATTCATGCTGAAAGGTCAAATGAGAGTTTAGTGGAAGCTTTTAAAAATATGCATGTACATGAAGAGATG
                                                                                |||| |||||    ||| |  |||||  |   |||||  ||||  |  |||| | |         ||  |  |  ||| ||| |         | ||||    ||||||| ||| |||| |||||| | || ||||||||||| || |||||||| ||| | ||||||| | | ||||||||||| |||| ||||||| |||||  ||||  |
------------------------------------------------------------------------------tagcttcaattgaacacatatagtgaaataaatagaagtaatgtcggtgctcatttgt---------attgtttttctttattgttct------gatgaaatcctgtttgaatagGGGTATTTATCCACCAGCTGAGGAGTACATTATCCATGCTGAGAGGCCCAATGAGACTCTGGTGGAAGCTTTCAAAAGTATGCATATACATCTAGAGGAG

upper sequence: GRMZM2G141587_T03 (Zea mays), 3'ss of exon 22
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 22
gtttttttgttctttttgtcttcatctataactgtatccttttgtattgtctctgattacctcttgcatcagatgatggcgctttaattgcgttcatctgttgaaa--atcggaagtggtgtcaatattcatatttttccaaactatcatcatcttttgttgatactcacaaaaagaaaattcgtttgaaaagGAGTATCTATCCATCGGCCGAGGAGTACATGATTCATGCTGAAAGGTCAAATGAGAGTTTAGTGGAAGCTTTTAAAAATATGCATGTACATGAAGAGATG
                                                                           ||   |||| | ||| |  ||| |  |||||  |   |||||  ||||| |  ||||            | |  |  |  ||| |||        || | ||||     |||| | ||| |||| ||| || | ||  |||||||||| || |||||||| ||| | || |||| | | ||||||||||| |||||||||| | ||||| |||||  |
---------------------------------------------------------------------------atttagcttcagttgagcacatatagtgaaataaatagaagtaatgtcagtgctcat-----------ttgtactttttctttattg-------taatatgaaatcctatttgtatagGGGTATTTATGCACCAGCTAAGGAGTACATTATCCATGCTGAGAGGCCTAACGAGACTCTGGTGGAAGCTTTCAAAAATATGCGTATACATCAAGAGGAG
















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|56382379|gb|CV985048.1|CV985048
EST:     GAAGACTGGCAGATTGCTCTCAACGTAGAAGCTGCTGTTGCCTCTAAAAG                         GAGTATCTATCCACCGGCCGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTCAACGTAGAAGCTGCTGTTGCCTCTAAAAGgtttttttgt ... gtttgaaaagGAGTATCTATCCATCGGCCGAGGAGTACATGATTCATGCTGAAAGGTCAAA
EST: gi|78114292|gb|DV532681.1|DV532681
EST:     GAAGACTGGCAGATTGCTCTCAACGTAGAAGCTGCTGTTGCCTCTAAAAG                         GAGTATCTATCCATCGGCCGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTCAACGTAGAAGCTGCTGTTGCCTCTAAAAGgtttttttgt ... gtttgaaaagGAGTATCTATCCATCGGCCGAGGAGTACATGATTCATGCTGAAAGGTCAAA
EST: gi|32795452|gb|CD947688.1|CD947688
EST:     GAAGACTGGCAGATTGCTCTCAACGTAGAAGCTGCTGTTGCCTCTAAAAG                         GAGTATCTATCCATCGGCCGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTCAACGTAGAAGCTGCTGTTGCCTCTAAAAGgtttttttgt ... gtttgaaaagGAGTATCTATCCATCGGCCGAGGAGTACATGATTCATGCTGAAAGGTCAAA
EST: gi|32793487|gb|CD945723.1|CD945723
EST:     GAAGACTGGCAGATTGCTCTCAACGTAGAAGCTGCTGTTGCCTCTAAAAG                         GAGTATCTATCCATCGGCCGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTCAACGTAGAAGCTGCTGTTGCCTCTAAAAGgtttttttgt ... gtttgaaaagGAGTATCTATCCATCGGCCGAGGAGTACATGATTCATGCTGAAAGGTCAAA
EST: gi|32808372|gb|CD960606.1|CD960606
EST:     GAAGACTGGCAGATTGCTCTCAACGTAGAAGCTGCTGTTGCCTCTAAAAG                         GAGTATCTATCCATCGGCCGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTCAACGTAGAAGCTGCTGTTGCCTCTAAAAGgtttttttgt ... gtttgaaaagGAGTATCTATCCATCGGCCGAGGAGTACATGATTCATGCTGAAAGGTCAAA
EST: gi|32791813|gb|CD944049.1|CD944049
EST:     GAAGACTGGCAGATTGCTCTCAACGTAGAAGCTGCTGTTGCCTCTAAAAG                         GAGTATCTATCCATCGGCCGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTCAACGTAGAAGCTGCTGTTGCCTCTAAAAGgtttttttgt ... gtttgaaaagGAGTATCTATCCATCGGCCGAGGAGTACATGATTCATGCTGAAAGGTCAAA
EST: gi|71438645|gb|DR819695.1|DR819695
EST:     GAAGACTGGCAGATTGCTCTCAACGTAGAAGCTGCTGTTGCCTCTAAAAG                         GAGTATCTATCCATCGGCCGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTCAACGTAGAAGCTGCTGTTGCCTCTAAAAGgtttttttgt ... gtttgaaaagGAGTATCTATCCATCGGCCGAGGAGTACATGATTCATGCTGAAAGGTCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaaactatcatcatcttttgttgatactcacaaaaagaaaattcgtttgaaaagGAGTATCTATCCATCGGCCGAGGAGTACATGATTCATGCTGAAAGGTCAAATGAGAGTTTAGTGGAAGCTTTTAAAAATATGCATGTACATGAAGAGATG
                         tactcac  putative branch site (score: 1)
                                          ttcgttt  putative PPT
                              acaaaaagaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttttttgttctttttgtcttcatctataactgtatccttttgtattgtctctgattacctcttgcatcagatgatggcgctttaattgcgttcatctgttgaaaatcggaagtggtgtcaatattcatatttttccaaactatcatcatcttttgttgatactcacaaaaagaaaattcgtttgaaaagGAGTATCTATCCATCGGCCGAGGAGTACATGATTCATGCTGAAAGGTCAAATGAGAGTTTAGTGGAAGCTTTTAAAAATATGCATGTACATGAAGAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG