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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGAGGCAGTCAAATTTCAAGTTACCTGCTGACCCATCCACTCCGATTATCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAGgtttgttttggcaaggagtccaatgggtgtatatttgcagttctgcttgagagcacctagcttaacttatccttccgctctctctattggcag

Basic information

species Zea mays
transcript GRMZM2G104294_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104294_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os04g55960.1 (Oryza sativa), 5'ss of exon 14
TGTGAGGCAGTCAAATTTCAAGTTACCTGCTGACCCATCCACTCCGATTATCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAGgtttgttttggcaaggagtccaatgggtgtatatttgcagttctgcttgagagcacctagcttaacttatccttccgctctctctattggcag
|||||||||||||||||| ||||| ||||| || ||  ||||||| |||||||||||||||||||| |||||| | || || |||||||| ||||||||||||||||||  |||    ||  ||   ||| || ||    ||     ||     |   |  ||| ||  |  ||  |||  |||         
TGTGAGGCAGTCAAATTTTAAGTTGCCTGCAGATCCGACCACTCCAATTATCATGATTGGTCCTGGTACAGGGTTAGCACCATTTAGAGGCTTCTTGCAGgtttgttttcccaaatcttc--atttctgtttactttggatttgagatggccctagtaactttatctgttatttatgcttgctcag-------

upper sequence: GRMZM2G104294_T02 (Zea mays), 5'ss of exon 8
lower sequence: EFJ20231 (Selaginella moellendorffii), 5'ss of exon 14
TGTGAGGCAGTCAAATTTCAAGTTACCTGCTGACCCATCCACTCCGATTATCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAGgtttgttttggcaaggagtccaatgggtgtatatttgcagttctgcttgagagcacctagcttaacttatccttccgctctctctattggcag
||| ||||| || |  |||||||| ||  |  |  |  |   ||| ||  | |||||||| ||||| |||||  | ||||||||||||||||| |||||||       ||   | | |||                    ||  |    | | ||  ||||  | | | |  |||  |               
TGTCAGGCAATCTACGTTCAAGTTGCCGTCAAAGTCCACTGTTCCTATAGTGATGATTGGACCTGGAACAGGCTTAGCTCCTTTTAGAGGTTTTTTGCAGg-------tgagcaagcgtc--------------------tttcgtcataaatcatttagcgcaccatgtttttctacag-------------
















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|32928790|gb|CF033602.1|CF033602
EST:     TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAG                         GAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAGTCCTT
genomic: TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAGgtttgttttg ... ctattggcagGAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTT
EST: gi|194716812|gb|FK933971.1|FK933971
EST:     TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAG                         GAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTT
genomic: TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAGgtttgttttg ... ctattggcagGAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTT
EST: gi|32921358|gb|CF026170.1|CF026170
EST:     TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAG-TTTCTTGCAA                         GAAAGGTTAGCACTGAAACAATC
genomic: TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAGgtttgttttg ... ctattggcagGAAAGGTTAGCACTGAAACAATC
EST: gi|32832538|gb|CD972216.1|CD972216
EST:     TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAG                         GAAAGGTTAGCACTGAAACAATCTGGAGC
genomic: TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAGgtttgttttg ... ctattggcagGAAAGGTTAGCACTGAAACAATCTGGAGC
EST: gi|32929828|gb|CF034640.1|CF034640
EST:     TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAG                         GAAAGGTTAGCACTGAAA
genomic: TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAGgtttgttttg ... ctattggcagGAAAGGTTAGCACTGAAA
EST: gi|67024128|gb|CO452877.1|CO452877
EST:     TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAN                         GAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTT
genomic: TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAGgtttgttttg ... ctattggcagGAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTT
EST: gi|211465905|gb|FL134197.1|FL134197
EST:     TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAG                         GAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTT
genomic: TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAGgtttgttttg ... ctattggcagGAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTT
EST: gi|32835489|gb|CD975167.1|CD975167
EST:     TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAG                         GAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTT
genomic: TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAGgtttgttttg ... ctattggcagGAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTT
EST: gi|32928791|gb|CF033603.1|CF033603
EST:     TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAG                         GAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTT
genomic: TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAGgtttgttttg ... ctattggcagGAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTT
EST: gi|32929541|gb|CF034353.1|CF034353
EST:     TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAG                         GAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTT
genomic: TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAGgtttgttttg ... ctattggcagGAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTT
EST: gi|32835138|gb|CD974816.1|CD974816
EST:     TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAG                         GAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTT
genomic: TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAGgtttgttttg ... ctattggcagGAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTT
EST: gi|61119293|gb|DN560254.1|DN560254
EST:     TCATGATTGGTCCTGGAACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAG                         GAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTT
genomic: TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAGgtttgttttg ... ctattggcagGAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTT
EST: gi|32921780|gb|CF026592.1|CF026592
EST:     TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAG                         GAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTT
genomic: TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAGgtttgttttg ... ctattggcagGAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTT
EST: gi|32920698|gb|CF025510.1|CF025510
EST:     TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAG                         GAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTT
genomic: TCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAGgtttgttttg ... ctattggcagGAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTT

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: 268

TGTGAGGCAGTCAAATTTCAAGTTACCTGCTGACCCATCCACTCCGATTATCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAGgtttgttttg ... ctattggcagGAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 401

TGTGAGGCAGTCAAATTTCAAGTTACCTGCTGACCCATCCACTCCGATTATCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAGgtttgttttg ... ctattggcagGAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 424

TGTGAGGCAGTCAAATTTCAAGTTACCTGCTGACCCATCCACTCCGATTATCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAGgtttgttttg ... ctattggcagGAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 469

TGTGAGGCAGTCAAATTTCAAGTTACCTGCTGACCCATCCACTCCGATTATCATGATTGGTCCTGGGACAGGGCTGGCTCCTTTTAGAGGTTTCTTGCAGgtttgttttg ... ctattggcagGAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG