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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacaacgaaatagtgagtaatgtcaagtagttccattacagcatctaatgccaataatgtgaagttatgaatgtcactaataacgaaatttcacttgtagACTGTGCTGCTATTTTCGTGCATCCTAGCATTTCTACTGAACTACACTATCTTCTGGAACACAATCCTGAATTCTGCACTCACACAATCGATGTGTGGGA

Basic information

species Zea mays
transcript GRMZM2G133226_T04
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133226_T04 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g40030.1 (Oryza sativa), 3'ss of exon 7
-gacaacgaaa--tagtgagtaatgtcaagtagttccat-tacagcatctaatgccaataatgtgaagttatgaatgtcactaataacgaaatttcacttgtagACTGTGCTGCTATTTTCGTGCATCCTAGCATTTCTACTGAACTACACTATCTTCTGGAACACAATCCTGAATTCTGCACTCACACAATCGATGTGTGGGA
  ||||  |    |  | | |   ||  || |||  ||  | || | |||  |     | |    ||| ||| ||| |||   || | |  ||| |  |||||| | ||||||||||| || ||||| ||||| ||||| || |||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| |
acacaatcatgcctgttcacttcagtggaggagtgacacatccaacttctgttattcttcaga--aagctatcaatatcat--atgatgttattccgattgtagGCGGTGCTGCTATTCTCATGCATGCTAGCTTTTCTGCTAAACTACACTATCTTCTGGAATACAATCCTGAATTCTGCACTCACACAATCGATGTGTGGTA
















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|71440135|gb|DR821185.1|DR821185
EST:     ACCTAAAGAGGGCCATGGAATTTCCGTACCTTTATTCCCCTGGGTTCATG                         ACTGTGCTGCTATTTTCGTGCATCCTAGCATTTTTACTGAACTACACTATC
genomic: ACCTAAAGAGGGCCATGGAATTTCCGTACCTTTATTCCCCTGGGTTCATGgtaacattaa ... tcacttgtagACTGTGCTGCTATTTTCGTGCATCCTAGCATTTCTACTGAACTACACTATC
EST: gi|148933234|gb|EC876885.2|EC876885
EST:     ACCTAAAGAGGGCCATGGAATTTCCGTACCTTTATTCCCCTGGGTTCATG                         ACTGTGCTGCTATTTTCGTGCATCCTAGCATTTCTACTGAACTACACTATC
genomic: ACCTAAAGAGGGCCATGGAATTTCCGTACCTTTATTCCCCTGGGTTCATGgtaacattaa ... tcacttgtagACTGTGCTGCTATTTTCGTGCATCCTAGCATTTCTACTGAACTACACTATC
EST: gi|149103657|gb|EE289061.2|EE289061
EST:     ACCTAAAGAGGGCCATGGAATTTCCGTACCTTTATTCCCCTGGGTTCATG                         ACTGTGCTGCTATTTTCGTGCATCCTAGCATTTCTACTGAACTACACTATC
genomic: ACCTAAAGAGGGCCATGGAATTTCCGTACCTTTATTCCCCTGGGTTCATGgtaacattaa ... tcacttgtagACTGTGCTGCTATTTTCGTGCATCCTAGCATTTCTACTGAACTACACTATC
EST: gi|148947033|gb|EC892330.2|EC892330
EST:     ACCTAAAGAGGGCCATGGAATTTCCGTACCTTTATTCCCCTGGGTTCATG                         ACTGTGCTGCTATTTTCGTGCATCCTAGCATTTCTACTGAACTACACTATC
genomic: ACCTAAAGAGGGCCATGGAATTTCCGTACCTTTATTCCCCTGGGTTCATGgtaacattaa ... tcacttgtagACTGTGCTGCTATTTTCGTGCATCCTAGCATTTCTACTGAACTACACTATC
EST: gi|91054598|gb|EB165016.1|EB165016
EST:     ACCTAAAGAGGGCCATGGAATTTCCGTACCTTTATTCCCCTGGGTTCATG                         ACTGTGCTGCTATTTTCGTGCATCCTAGCATTTCTACTGAACTACACTATC
genomic: ACCTAAAGAGGGCCATGGAATTTCCGTACCTTTATTCCCCTGGGTTCATGgtaacattaa ... tcacttgtagACTGTGCTGCTATTTTCGTGCATCCTAGCATTTCTACTGAACTACACTATC

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: 48 (upstream exon), 46 (downstream exon)
Score: 52

GACTTGTCTGTGGACCTTCAGTACTGTTATTGACATATATTCAGGGTGACCTAAAGAGGGCCATGGAATTTCCGTACCTTTATTCCCCTGGGTTCATGgtaacattaa ... tcacttgtagACTGTGCTGCTATTTTCGTGCATCCTAGCATTTCTACTGAACTACACTATCTTCTGGAACACAATCCTGAATTCTGCACTCACACAATCGATGTGTGGGA


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 53

GACTTGTCTGTGGACCTTCAGTACTGTTATTGACATATATTCAGGGTGACCTAAAGAGGGCCATGGAATTTCCGTACCTTTATTCCCCTGGGTTCATGgtaacattaa ... tcacttgtagACTGTGCTGCTATTTTCGTGCATCCTAGCATTTCTACTGAACTACACTATCTTCTGGAACACAATCCTGAATTCTGCACTCACACAATCGATGTGTGGGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 117

GACTTGTCTGTGGACCTTCAGTACTGTTATTGACATATATTCAGGGTGACCTAAAGAGGGCCATGGAATTTCCGTACCTTTATTCCCCTGGGTTCATGgtaacattaa ... tcacttgtagACTGTGCTGCTATTTTCGTGCATCCTAGCATTTCTACTGAACTACACTATCTTCTGGAACACAATCCTGAATTCTGCACTCACACAATCGATGTGTGGGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 41

GACTTGTCTGTGGACCTTCAGTACTGTTATTGACATATATTCAGGGTGACCTAAAGAGGGCCATGGAATTTCCGTACCTTTATTCCCCTGGGTTCATGgtaacattaa ... tcacttgtagACTGTGCTGCTATTTTCGTGCATCCTAGCATTTCTACTGAACTACACTATCTTCTGGAACACAATCCTGAATTCTGCACTCACACAATCGATGTGTGGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatgccaataatgtgaagttatgaatgtcactaataacgaaatttcacttgtagACTGTGCTGCTATTTTCGTGCATCCTAGCATTTCTACTGAACTACACTATCTTCTGGAACACAATCCTGAATTCTGCACTCACACAATCGATGTGTGGGA
                                taataac  putative branch site (score: 41)
                                           tttcactt  putative PPT
                                taataacgaaattt  TA-rich tract