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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctgattccgttctctgcttaacaatttccaaatccgatttgctcctgcagtccgttatctctaatatctgtggcttcccctctctcagGTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACGAGGGATACGCCCTCCCCCACGCCATCCTTCGTCTTGACCTGGCCGGTCG

Basic information

species Zea mays
transcript GRMZM2G152328_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152328_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g50885.1 (Oryza sativa), 3'ss of exon 2
gtgagctgattccgttctctgcttaacaatt-tccaaatccgatttgctcctgcagtccgttat-ctctaat-----atctgtggcttcccctctctcagGTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACGAGGGATACGCCCTCCCCCACGCCATCCTTCGTCTTGACCTGGCCGGTCG
 | |   || ||   | |   | |   |||| |        |   ||||    || |  | | | ||  | |     ||   ||  || || | || ||||||| ||| | ||||| || |||||||| |||||||| ||||||||||| || ||||| || |||||||| || ||||||||||| ||||| || || ||
ataaatggaatcatgtttgaacatcctaattctgttggcatggagtgctttgacattttgatgtgctacagttgtgaataactgaatttccttttcccagGTATTGTGTTGGACTCTGGTGATGGTGTCAGCCACACTGTCCCCATCTATGAAGGATATGCTCTCCCCCATGCTATCCTTCGTCTCGACCTTGCTGGGCG

upper sequence: GRMZM2G152328_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------------------gtgagctgattccgttctctgcttaacaatttccaaatccgatttgctcctgcagtccgttatctctaatatctgtggcttcccctctct-cagGTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACGAGGGATACGCCCTCCCCCACGCCATCCTTCGTCTTGACCTGGCCGGTCG
                                                                   |||    | |   ||  |   | |   ||  |        |  | |       |  | |  | |  |  |     ||  | |    |  | ||||||||||||| |||   ||||||||||||| |||||| || || ||||||||||| ||||| || || ||||||||  | ||  | ||| |||| |||||
gtgagtgatgggagaaggggtgaggtgaatgcagcatgtgcgttggttgcgaaagtggtggaggtgtgtggagaggtggggtgtttgacatgggaaggtttg----tgggtcggggtaagaaactgagagcagttgtggtgatgaatgcaatgcaatgcagGTATCGTGCTGGACAGTGGAGATGGTGTGACCCACACGGTGCCAATCTACGAGGGTTACGCACTGCCTCACGCCATATTGCGATTAGACTTGGCGGGTCG
















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|6918758|gb|AW400288.1|AW400288
EST:     CGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAG                         GTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACG
genomic: CGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAGgtgagctgat ... cctctctcagGTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACG
EST: gi|7145305|gb|AW506786.1|AW506786
EST:     CGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAG                         GTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACG
genomic: CGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAGgtgagctgat ... cctctctcagGTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACG
EST: gi|6095303|gb|AW119970.1|AW119970
EST:     GGCCGTACCACAG                         GTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACG
genomic: GGCCGTACCACAGgtgagctgat ... cctctctcagGTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACG
EST: gi|211520844|gb|FL034051.1|FL034051
EST:     CGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAG                         GTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACA-CGTCCCCATCTACG
genomic: CGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAGgtgagctgat ... cctctctcagGTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACG
EST: gi|78180780|gb|DV551153.1|DV551153
EST:     CGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAG                         GTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACG
genomic: CGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAGgtgagctgat ... cctctctcagGTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACG
EST: gi|67017533|gb|CO446282.1|CO446282
EST:     CGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAG                         GTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACG
genomic: CGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAGgtgagctgat ... cctctctcagGTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACG

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: 216

GAGAAGATGACCCAGATCATGTTCGAGACCTTCAACACCCCGGCTATGTACGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAGgtgagctgat ... cctctctcagGTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACGAGGGATACGCCCTCCCCCACGCCATCCTTCGTCTTGACCTGGCCGGTCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 38

GAGAAGATGACCCAGATCATGTTCGAGACCTTCAACACCCCGGCTATGTACGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAGgtgagctgat ... cctctctcagGTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACGAGGGATACGCCCTCCCCCACGCCATCCTTCGTCTTGACCTGGCCGGTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 26

GAGAAGATGACCCAGATCATGTTCGAGACCTTCAACACCCCGGCTATGTACGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAGgtgagctgat ... cctctctcagGTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACGAGGGATACGCCCTCCCCCACGCCATCCTTCGTCTTGACCTGGCCGGTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 540

GAGAAGATGACCCAGATCATGTTCGAGACCTTCAACACCCCGGCTATGTACGTCGCCATCCAGGCCGTGCTCTCTCTGTATGCCAGTGGCCGTACCACAGgtgagctgat ... cctctctcagGTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACGAGGGATACGCCCTCCCCCACGCCATCCTTCGTCTTGACCTGGCCGGTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgatttgctcctgcagtccgttatctctaatatctgtggcttcccctctctcagGTATCGTGCTCGACTCGGGAGATGGTGTGAGCCACACCGTCCCCATCTACGAGGGATACGCCCTCCCCCACGCCATCCTTCGTCTTGACCTGGCCGGTCG
                         ctctaat  putative branch site (score: 540)
                                     tggcttcccctctctc  putative PPT
                          tctaatat  TA-rich tract