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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattatgatttgtcttctttacagctcaatggtattgcttgtctttttagactttctcattgtttgaaagtgagcatgattacgtaatggtattctatagGTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCCCAAAGTTCAGACAATGGTTCAACTTCAAGTCCGGGTACCAGTAGTTGCA

Basic information

species Zea mays
transcript GRMZM2G069631_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 4
aattatgatttgtcttctttacagctcaatggtattgcttgtctttttagactttctcatt---gtttgaaagtgagcatg-attac-gtaatggtat-tctatagGTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCCCAAAGTTCAGACAATGGTTCAACTTCAAGTCCGGGTACCAGTAGTTGCA
        |||   || ||| ||   | ||    ||  || | | |||||   || | | |   | |    |||    ||  ||||| ||  |  ||| | || |||| |||||||  || || |||||  ||||||||||||||||| | ||||| |||||||||| ||||||  ||||||| ||| |  | | ||||||||  |
-----cagttttaattatttgca-tgctatctctttctttctttgtttagctcttattacttaagctatgtagtatcaatacattacagttttactatctgtacagGTGCAAGAGAGGAAAGTAAAACGAATTTCAGTGATGAATTTGAATACCTCTCAAAGTTCAGGCAATGGCACAACTTCTAGTTCAAGCAGCAGTAGTTCTA
















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|211079477|gb|FL398611.1|FL398611
EST:     AATCAAGTATTGGAAG                         GTTCAAGAGAAAAAGGTGAAACGGGTTTCAGTGATGAATTTGGACACCTCC
genomic: AATCAAGTATTGGAAGgtatgtataa ... tattctatagGTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCC
EST: gi|211374954|gb|FL429396.1|FL429396
EST:     AATCAAGTATTGGAAG                         GTTCAAGAGAAAAAGGTGAAACGGGTTTCAGTGATGAATTTGGACACCTCC
genomic: AATCAAGTATTGGAAGgtatgtataa ... tattctatagGTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCC
EST: gi|67012325|gb|CO441074.1|CO441074
EST:     ATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAG                         GTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCC
genomic: ATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAGgtatgtataa ... tattctatagGTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCC
EST: gi|60340196|gb|DN207169.1|DN207169
EST:     ATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAG                         GTTCAAGAGAAAAAGGTGAAACGGGTTTCAGTGATGAATTTGGACACCTCC
genomic: ATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAGgtatgtataa ... tattctatagGTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCC
EST: gi|148939774|gb|EC884472.2|EC884472
EST:     ATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAG                         GTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCC
genomic: ATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAGgtatgtataa ... tattctatagGTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCC
EST: gi|148991720|gb|EE033282.2|EE033282
EST:     ATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAG                         GTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCC
genomic: ATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAGgtatgtataa ... tattctatagGTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCC
EST: gi|94472892|gb|EB701850.1|EB701850
EST:     ATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAG                         GTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCC
genomic: ATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAGgtatgtataa ... tattctatagGTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCC

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: 45 (upstream exon), 45 (downstream exon)
Score: 127

GGAAATAGAAGAGAAGATTAACAAGATCAAGTGGTGCCAAACAACCAACAATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAGgtatgtataa ... tattctatagGTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCCCAAAGTTCAGACAATGGTTCAACTTCAAGTCCGGGTACCAGTAGTTGCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 163

GGAAATAGAAGAGAAGATTAACAAGATCAAGTGGTGCCAAACAACCAACAATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAGgtatgtataa ... tattctatagGTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCCCAAAGTTCAGACAATGGTTCAACTTCAAGTCCGGGTACCAGTAGTTGCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 150

GGAAATAGAAGAGAAGATTAACAAGATCAAGTGGTGCCAAACAACCAACAATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAGgtatgtataa ... tattctatagGTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCCCAAAGTTCAGACAATGGTTCAACTTCAAGTCCGGGTACCAGTAGTTGCA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 133

GGAAATAGAAGAGAAGATTAACAAGATCAAGTGGTGCCAAACAACCAACAATGCACTCTTTCTCTTGTCTACAAATGACAAAACAATCAAGTATTGGAAGgtatgtataa ... tattctatagGTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCCCAAAGTTCAGACAATGGTTCAACTTCAAGTCCGGGTACCAGTAGTTGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagactttctcattgtttgaaagtgagcatgattacgtaatggtattctatagGTTCAAGAGAAAAAGGTGAAACGCGTTTCAGTGATGAATTTGGACACCTCCCAAAGTTCAGACAATGGTTCAACTTCAAGTCCGGGTACCAGTAGTTGCA
                                             tattctata  TA-rich tract