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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAGCTCTATGAAGACAATGAGTACGCACTCTACACCATAACACTTTTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTCCAGgtaaggtttccttggacacattatgcttttttttttacattgatctggcaacccatctttagtcttttgccattcactaagtttcattcgctttgttccag

Basic information

species Zea mays
transcript GRMZM2G177912_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177912_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 7
ACAGCTCTATGAAGACAATGAGTACGCACTCTACACCATAACACTTTTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTCCAGgtaaggtttccttggacacattatgcttttttttttacattgatctggca-acccatctttagtcttttgccattcactaagtttcattcgctttgttccag-------------------------------------------------------------------------------
| | || ||||| ||||||||||| || ||||||||  ||||| | ||||||||||||||||||||||||||||||||||| || || || |||||||||||||  || || |    || || |  |        |   || |     || |   | ||||  ||  | |    | |   |||| ||      |||   |||                                                                               
AAAACTTTATGAGGACAATGAGTATGCTCTCTACACGGTAACATTGTTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCACGTGAAAAAGGTTTCCAGgtaaatttgccgtcctaactttttcatcaaaaacctttgtttacacttcacatttagcttttatccctagagccttag-gagttccaaataacttgggacagaaattcagtcttgtttttctgtccccatcaatctggcaattctctgtcacccattaacttgtattacgttgaaatacag
















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|148969237|gb|EE019991.2|EE019991
EST:     CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTCCAG                         GTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAG
genomic: CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTCCAGgtaaggtttc ... tttgttccagGTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAG
EST: gi|76288289|gb|DV027857.1|DV027857
EST:     ACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTCCAG                         GTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAG
genomic: ACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTCCAGgtaaggtttc ... tttgttccagGTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAG
EST: gi|67016433|gb|CO445182.1|CO445182
EST:     CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTNCAG                         ATTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGT
genomic: CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTCCAGgtaaggtttc ... tttgttccagGTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGT
EST: gi|60340364|gb|DN207337.1|DN207337
EST:     CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTCCAG                         GTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAG
genomic: CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTCCAGgtaaggtttc ... tttgttccagGTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAG
EST: gi|37397643|gb|CF636126.1|CF636126
EST:     CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTCCAG                         GTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAG
genomic: CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTCCAGgtaaggtttc ... tttgttccagGTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAG
EST: gi|71327561|gb|DR800389.1|DR800389
EST:     TAAGGTTGTTGACAACTTTAAAGGTCCGTGCTCGCGAGAAGGGTTTCCAG                         GTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAG
genomic: TAAGGTTGTTGACAACTTT-AAGGTCCGTGCTCGCGAGAAGGGTTTCCAGgtaaggtttc ... tttgttccagGTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAG
EST: gi|40337132|gb|CK371202.1|CK371202
EST:     CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTCCAG                         GTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAG
genomic: CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTCCAGgtaaggtttc ... tttgttccagGTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAG

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), 49 (downstream exon)
Score: 129

ACAGCTCTATGAAGACAATGAGTACGCACTCTACACCATAACACTTTTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTCCAGgtaaggtttc ... tttgttccagGTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAGATGGAGAAGTTACTGCTAGAGCAGGAAGTTATGAGGACCTCGCTTCTGC


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 206

ACAGCTCTATGAAGACAATGAGTACGCACTCTACACCATAACACTTTTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTCCAGgtaaggtttc ... tttgttccagGTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAGATGGAGAAGTTACTGCTAGAGCAGGAAGTTATGAGGACCTCGCTTCTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 232

ACAGCTCTATGAAGACAATGAGTACGCACTCTACACCATAACACTTTTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTCCAGgtaaggtttc ... tttgttccagGTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAGATGGAGAAGTTACTGCTAGAGCAGGAAGTTATGAGGACCTCGCTTCTGC


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 134

ACAGCTCTATGAAGACAATGAGTACGCACTCTACACCATAACACTTTTTGCTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTCCAGgtaaggtttc ... tttgttccagGTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAGATGGAGAAGTTACTGCTAGAGCAGGAAGTTATGAGGACCTCGCTTCTGC