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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaagcgttagtttgattgttcattccacatgtttctgcggtaaagtagatgttttggtatggaccttagatgcaactcgtggtttgactatttctagaa...

Basic information

species Zea mays
transcript GRMZM2G141903_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141903_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g55389.1 (Oryza sativa), 5'ss of exon 6
ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaagcgttagtttgattgtt-cattccacatgtttctgcggtaaagtagatgttttggtatggaccttagatgcaactcgtggtttgact-atttctagaa
||||| |||||||| |||||||| ||||| ||||| |||||||| |||||||| ||||| |||||||||||    ||||||||| |  | |  ||||| | ||   || |||  | ||| |||||||||     || |      | ||  |   |||  | | | | |
ATATTCCGCAAGGAGCCATTCTTCTATGGTCATGATAACCATGATCAACTTGTCAAGATCGCAAAGgtaagtcccagtttgattctggcctctcacatttctcaagggaaaaa-aaatggtttggtatgcctgataaa-atgtttagttatgcaactcgtgttttgga

upper sequence: GRMZM2G141903_T01 (Zea mays), 5'ss of exon 6
lower sequence: PP1S165_107V6.1 (Physcomitrella patens), 5'ss of exon 6
ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaagc-----gttagtttgattgttcat-tccacatgtttctgcggtaaagtagatgttttggtatggaccttagatgcaactcgtggtttgact-atttctagaa
|| || |||||||| || || || |||||||| |||||  |||| |||||||||||||||||||||| ||||     ||    | | ||| | |  | || | |  | | |  |||  || |||  ||   ||     |||| |      |||    |   |   |||| || 
ATTTTCCGCAAGGAGCCGTTTTTCTATGGCCACGACAATTATGATCAACTTGTGAAGATTGCAAAGgcaagctcattgtcctctgggttgattaccttcataagcgttttc--taatctacatggattaaaata----ttaggttttgtacgtcacatattttgcttctgga-

upper sequence: GRMZM2G141903_T01 (Zea mays), 5'ss of exon 6
lower sequence: PP1S63_208V6.1 (Physcomitrella patens), 5'ss of exon 7
ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaagcgttagtttgattgttcat------tccacatgtttctgcggtaaagtagatgttttggtatgga---ccttagatgcaactcgtggtt-tgactatttctagaa----------------------------------
|| ||||| ||||| |||||||||||||| ||||||||  |||| || |||||||||||||| |||||   ||  | | | |||    ||      || |   ||  ||||      |||  | || ||    |     |||    ||   |||  ||   ||  ||  |||                                      
ATCTTTCGGAAGGAGCCATTCTTTTATGGACATGACAATTATGATCAGCTTGTGAAGATTGCCAAGgtgctcggaaatctcatttactatcagccttcaatcagtcactgctcattcgtaatttttctgaatcgtttctcctcctgtgtttctcaaggccatgtttaaatcttcgttctaaatctaatctttgttgttacctgaaatcag

upper sequence: GRMZM2G141903_T01 (Zea mays), 5'ss of exon 6
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 7
ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgta-agcgttagtttgattgttcattccacatgtttctgcggtaaagtagatgttttggtatggaccttagatgcaactcgtggtttgactatttctagaa------------------------------------------------
|||||||| ||||| |||||||||||||| ||||||||  |||| ||||||||||||||||| |||||  || |  ||||      |  |||   |   ||   || || |  || ||   ||  |||  |  ||  ||  ||   ||  | | ||| | | | | |                                                
ATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAGgtgcagtggcagttcatacatagatttgcc---ttcaagcagtta--tatatcactttttatttattttgtataaaaa--gtcatattactgtctttcgcaacgccaagttgtgttttgagccttatctttgtgggtgtctgataccag

upper sequence: GRMZM2G141903_T01 (Zea mays), 5'ss of exon 6
lower sequence: EFJ20478 (Selaginella moellendorffii), 5'ss of exon 6
ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgt---aagcgttagtttgattgttcattccacatgtttctgcggtaaagtagatgt-tttggtatggaccttagatgcaactcgtggtttgactatttctagaa
||||||||||| |||||||||||||||||||||||||| || || || || ||||||||||| |||||   || ||  ||  ||  ||||  || |   ||||| ||  ||    | |  || ||| |                                          
ATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTGGTGAAGATTGCCAAGgttttaaacgc-agaatgtctgtttcttgc---tgtttttgacgttggcttgtggtgtttag------------------------------------------

upper sequence: GRMZM2G141903_T01 (Zea mays), 5'ss of exon 6
lower sequence: EFJ28543 (Selaginella moellendorffii), 5'ss of exon 6
ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgta--agcgttagtttgattgttcattccacatgtttctgcggtaaagtagatgt-tttggtatggaccttagatgcaactcgtggtttgactatttctagaa
||||||||||| |||||||||||||||||||||||||| || || || || ||||||||||| |||||   |     ||  ||  ||||  || |   ||||| ||  ||    | |  || ||| |                                          
ATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTGGTGAAGATTGCCAAGgttttaaacccagaatgtctgtttgttgc---tgtttttgacgttggcttgtggtgtttag------------------------------------------

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|149107620|gb|EE189502.2|EE189502
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGCTGAATTCTTATTTGAACAAGTACCACATTGAG
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaagcgtta ... tatttttcagGTCCTTGGAACAGATGGGCTGAATTCTTATTTGAACAAGTACCACATTGAG
EST: gi|18964717|gb|BM661166.1|BM661166
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACNTGTGAAGATTGCAAAG                         GTCCTNGGAACAGATGGGCTGAATTCTTATTTGAACAAGTACCACATTGAG
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaagcgtta ... tatttttcagGTCCTTGGAACAGATGGGCTGAATTCTTATTTGAACAAGTACCACATTGAG
EST: gi|78027572|gb|DV495959.1|DV495959
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGCTGAATTCTTATTTGAACAAGTACCACATTGAG
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaagcgtta ... tatttttcagGTCCTTGGAACAGATGGGCTGAATTCTTATTTGAACAAGTACCACATTGAG
EST: gi|76925598|gb|DV170499.1|DV170499
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGCTGAATTCTTATTTGAACAAGTACCACATTGAG
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaagcgtta ... tatttttcagGTCCTTGGAACAGATGGGCTGAATTCTTATTTGAACAAGTACCACATTGAG
EST: gi|60353291|gb|DN220264.1|DN220264
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGCTGAATTCTTATTTGAACAAGTACCACATTGAG
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaagcgtta ... tatttttcagGTCCTTGGAACAGATGGGCTGAATTCTTATTTGAACAAGTACCACATTGAG
EST: gi|60400467|gb|DN233274.1|DN233274
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGCTGAATTCTTATTTGAACAAGTACCACATTGAG
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaagcgtta ... tatttttcagGTCCTTGGAACAGATGGGCTGAATTCTTATTTGAACAAGTACCACATTGAG
EST: gi|5895649|gb|AW036895.1|AW036895
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGCTGAATTCTTATTTGAACAAGTACCACATTGAG
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaagcgtta ... tatttttcagGTCCTTGGAACAGATGGGCTGAATTCTTATTTGAACAAGTACCACATTGAG
EST: gi|60344732|gb|DN211705.1|DN211705
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGCTGAATTCTTATTTGAACAAGTACCACATTGAG
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaagcgtta ... tatttttcagGTCCTTGGAACAGATGGGCTGAATTCTTATTTGAACAAGTACCACATTGAG
EST: gi|24769466|gb|CA404595.1|CA404595
EST:     TTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGCTGAATTCTTATTTGAACAAGTACCACATTGAG
genomic: TTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaagcgtta ... tatttttcagGTCCTTGGAACAGATGGGCTGAATTCTTATTTGAACAAGTACCACATTGAG
EST: gi|60394565|gb|DN227435.1|DN227435
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGCTGAATTCTTATTTGAACAAGTACCACATTGAG
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaagcgtta ... tatttttcagGTCCTTGGAACAGATGGGCTGAATTCTTATTTGAACAAGTACCACATTGAG
EST: gi|5819188|gb|AI987394.1|AI987394
EST:     TTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGCTGAATTCTTATTTGAACAAGTACCACATTGAG
genomic: TTGTGAAGATTGCAAAGgtaagcgtta ... tatttttcagGTCCTTGGAACAGATGGGCTGAATTCTTATTTGAACAAGTACCACATTGAG
EST: gi|19351815|gb|BM896347.1|BM896347
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGCTGAATTCTTATTTGAAC
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaagcgtta ... tatttttcagGTCCTTGGAACAGATGGGCTGAATTCTTATTTGAAC
EST: gi|78021390|gb|DV489777.1|DV489777
EST:     TGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGCTGAATTCTTATTNGAACAAGTACCACATTGAG
genomic: TGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaagcgtta ... tatttttcagGTCCTTGGAACAGATGGGCTGAATTCTTATTTGAACAAGTACCACATTGAG
EST: gi|32849417|gb|CD989098.1|CD989098
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGCTGAATTCTTATTTGAACAAGTA
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaagcgtta ... tatttttcagGTCCTTGGAACAGATGGGCTGAATTCTTATTTGAACAAGTA
EST: gi|60399542|gb|DN232353.1|DN232353
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGCTGAATTCTTATTTGAACAAGTACCACATTGAG
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaagcgtta ... tatttttcagGTCCTTGGAACAGATGGGCTGAATTCTTATTTGAACAAGTACCACATTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaagcgttagtttgattgttcattccacatgtttctgcggtaaagtagatgttttggtatggaccttagatgcaactcgtggtttgactatttctagaa

- - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG