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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTGGGGGAAAATCAAAGGGACAAGGAACCTGAAATGTTCTCATTGTTACTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgactttgtgcagtgactactttgacacaacaactgcttgcctagtacataagttttgctcatgttttgagaatacaactgcttgctagcacata...

Basic information

species Zea mays
transcript GRMZM2G136296_T01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G136296_T02 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os02g32350.1 (Oryza sativa), 5'ss of exon 15
TTCTGGGGGAAAATCAAAGGGACAAGGAACCTGAAATGTTCTCATTGTTACTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtg--------------actttgtgca--gtgactactttgacacaacaactgcttgcctagtacataagttttgctcatgttttgagaatacaactgcttgctagcacata---------------------------------------------------------------------------------
|||||| ||||| || ||||||||||| ||  ||| | |||| |||||||| || ||||| || ||||||||||  ||||| ||||||||||||||||||||| |||              || || || |  |||   |  || |   |      | ||  ||  | ||||   |    |||  | |  |   |||      |||||      |                                                                                  
TTCTGGTGGAAAGTCCAAGGGACAAGGCACTGGAACTATTCTGATTGTTACACTGGTTGACGCAGAGACAGAAACCAGCATCAATGCTACCATGCTTGAGgttcgtgctacttgctacttaacattatgaattgtggtgatcttaaattagttgtcggttagcttctgcatagtctgctgtcacatatgaatgctactcaacattgcttctgtttgagattgaaggctgcttgcaaactagtcacagagatatgtgaaattgtcttcgttgctaatattcccattctgtttatgcag
















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|9461359|gb|BE453694.1|BE453694
EST:     AGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: AGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|18163487|gb|BM333326.1|BM333326
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGA
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|67017261|gb|CO446010.1|CO446010
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|4775850|gb|AI664855.1|AI664855
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|60396449|gb|DN229318.1|DN229318
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|211435102|gb|FL442353.1|FL442353
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|32847083|gb|CD986764.1|CD986764
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|211269150|gb|FL294986.1|FL294986
EST:     CAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|37393345|gb|CF633935.1|CF633935
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|40336444|gb|CK370514.1|CK370514
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|78025893|gb|DV494280.1|DV494280
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|5607972|gb|AI901639.1|AI901639
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|32944015|gb|CF048834.1|CF048834
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATACTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|29945603|gb|CB815724.1|CB815724
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|40334952|gb|CK369022.1|CK369022
EST:     AGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: AGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|20802346|gb|BQ293396.1|BQ293396
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTGCCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|211486828|gb|FL010663.1|FL010663
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|108953432|gb|EC364740.1|EC364740
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|33093747|gb|CF053741.1|CF053741
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGGGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|37382079|gb|CF627962.1|CF627962
EST:     AGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: AGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|5455714|gb|AI833404.1|AI833404
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|15080370|gb|BI389038.1|BI389038
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|32911048|gb|CF015860.1|CF015860
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|60357472|gb|DN224445.1|DN224445
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 148

TTCTGGGGGAAAATCAAAGGGACAAGGAACCTGAAATGTTCTCATTGTTACTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGGAAGACGGCTCTCCAGAACCTGGAACAGTTCCAGGAGAAGGCAAAGAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 85

TTCTGGGGGAAAATCAAAGGGACAAGGAACCTGAAATGTTCTCATTGTTACTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGGAAGACGGCTCTCCAGAACCTGGAACAGTTCCAGGAGAAGGCAAAGAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 53

TTCTGGGGGAAAATCAAAGGGACAAGGAACCTGAAATGTTCTCATTGTTACTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGGAAGACGGCTCTCCAGAACCTGGAACAGTTCCAGGAGAAGGCAAAGAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 197

TTCTGGGGGAAAATCAAAGGGACAAGGAACCTGAAATGTTCTCATTGTTACTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGGAAGACGGCTCTCCAGAACCTGGAACAGTTCCAGGAGAAGGCAAAGAAGG