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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAGCTGGGGCTTCGCCGAGGTGCCACAGATAATGACAAATTACAGACAGAAGTCAACAGAAGGACTCTCTGTCGCTTTTCTTATGACCTGGATTGTTGGgtatgctgtttcagatgtcttatgctccttggaactggatgcgattatattatttcacatgtcttgggctccttgcatgtgatttatatcatgtctcgataattgtacttatacctcgatgttaagcgtggatccctatataattccatcttatgcttctatgattgtgcag

Basic information

species Zea mays
transcript GRMZM2G024733_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024733_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g16170.4 (Oryza sativa), 5'ss of exon 2
TAAGCTGGGGCTTCGCCGAGGTGCCACAGATAATGACAAATTACAGACAGAAGTCAACAGAAGGACTCTCTGTCGCTTTTCTTATGACCTGGATTGTTGGgtatgctgtttcag---atgtcttatgctccttggaactggatgcgattatattatttcacatgtcttgggctccttgcatgtgatttatatcatgtctcgataattgtacttatacctcgatgttaa-gcgtggatccctatataattccatcttatgcttctatgattgtgcag
| ||||||||  | || |||||||||||||| || || |||||||  || |||||||||||||| || ||  | |||||||| ||||| |||||||||||||  ||  |||||     |  || ||| | || |||     || | | ||   |||   |  |||  | | |   ||  |||||    ||    || || |||  |    ||| |||    |||  |   ||  |                                         
TCAGCTGGGGAGTTGCTGAGGTGCCACAGATCATAACTAATTACAAGCATAAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGGgtgagccatttcatcacgttcctgatgtttctaggagacttatactactaatatataatatttgtagttgacagttt-tatgtg--caatgcagtg-cttgatgttct--cttgtactcttatgccattacgcag-----------------------------------------
















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|71426414|gb|DR807464.1|DR807464
EST:     AAGTCAACAGAAGGACTCTCTGTCGCTTTTCTTATGACCTGGATTGTTGG                         GGATTTGTTTAACCTTGTTGGCTGCTTCCTCGAACCTGCTACT
genomic: AAGTCAACAGAAGGACTCTCTGTCGCTTTTCTTATGACCTGGATTGTTGGgtatgctgtt ... gattgtgcagGGATTTGTTTAACCTTGTTGGCTGCTTCCTCGAACCTGCTACT
EST: gi|71432685|gb|DR813735.1|DR813735
EST:     AAGTCAACAGAAGGACTCTCTGTCGCTTTTCTTATGACCTGGATTGTTGG                         GGATTTGTTTAACCTTGTTGGCTGCTTCCTCGAACCTGCTACT
genomic: AAGTCAACAGAAGGACTCTCTGTCGCTTTTCTTATGACCTGGATTGTTGGgtatgctgtt ... gattgtgcagGGATTTGTTTAACCTTGTTGGCTGCTTCCTCGAACCTGCTACT
EST: gi|88752265|gb|DY536406.1|DY536406
EST:     AAGTCAACAGAAGGACTCTCTGTCGCTTTTCTTATGACCTGGATTGTTGG                         GGATTTGTTTAACCTTGTTGGCTGCTTCCT
genomic: AAGTCAACAGAAGGACTCTCTGTCGCTTTTCTTATGACCTGGATTGTTGGgtatgctgtt ... gattgtgcagGGATTTGTTTAACCTTGTTGGCTGCTTCCT
EST: gi|71770193|gb|DR968130.1|DR968130
EST:     AAGTCAACAGAAGGACTCTCTGTCGCTTTTCTTATGACCTGGATTGTTGG                         GGATTTGTTTAACCTTGTTGGCTGCTTCCTCGAACCTGCTACT
genomic: AAGTCAACAGAAGGACTCTCTGTCGCTTTTCTTATGACCTGGATTGTTGGgtatgctgtt ... gattgtgcagGGATTTGTTTAACCTTGTTGGCTGCTTCCTCGAACCTGCTACT
EST: gi|94472307|gb|EB701265.1|EB701265
EST:     AAGTCAACAGAAGGACTCTCTGTCGCTTTTCTTATGACCTGGATTGTTGG                         GGATTTGTTTAACCTTGTTGGCTGCTTCCTCGAACCTGCTACT
genomic: AAGTCAACAGAAGGACTCTCTGTCGCTTTTCTTATGACCTGGATTGTTGGgtatgctgtt ... gattgtgcagGGATTTGTTTAACCTTGTTGGCTGCTTCCTCGAACCTGCTACT
EST: gi|76288325|gb|DV027893.1|DV027893
EST:     AAGTCAACAGAAGGACTCTCTGTCGCTTTTCTTATGACCTGGATTGTTGG                         GGATTTGTTTAACCTTGTTGGCTGCTTCCTCGAACCTGCTACT
genomic: AAGTCAACAGAAGGACTCTCTGTCGCTTTTCTTATGACCTGGATTGTTGGgtatgctgtt ... gattgtgcagGGATTTGTTTAACCTTGTTGGCTGCTTCCTCGAACCTGCTACT

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), 43 (downstream exon)
Score: 49

TAAGCTGGGGCTTCGCCGAGGTGCCACAGATAATGACAAATTACAGACAGAAGTCAACAGAAGGACTCTCTGTCGCTTTTCTTATGACCTGGATTGTTGGgtatgctgtt ... gattgtgcagGGATTTGTTTAACCTTGTTGGCTGCTTCCTCGAACCTGCTACT


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 27

TAAGCTGGGGCTTCGCCGAGGTGCCACAGATAATGACAAATTACAGACAGAAGTCAACAGAAGGACTCTCTGTCGCTTTTCTTATGACCTGGATTGTTGGgtatgctgtt ... gattgtgcagGGATTTGTTTAACCTTGTTGGCTGCTTCCTCGAACCTGCTACT


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 15

TAAGCTGGGGCTTCGCCGAGGTGCCACAGATAATGACAAATTACAGACAGAAGTCAACAGAAGGACTCTCTGTCGCTTTTCTTATGACCTGGATTGTTGGgtatgctgtt ... gattgtgcagGGATTTGTTTAACCTTGTTGGCTGCTTCCTCGAACCTGCTACT


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 47

TAAGCTGGGGCTTCGCCGAGGTGCCACAGATAATGACAAATTACAGACAGAAGTCAACAGAAGGACTCTCTGTCGCTTTTCTTATGACCTGGATTGTTGGgtatgctgtt ... gattgtgcagGGATTTGTTTAACCTTGTTGGCTGCTTCCTCGAACCTGCTACT