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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCCACCGCGGCGGCGGTTGCAGCGATGGGGTCCATGACGATCGGTGCCAAGTACAAGACCACGATCAAGGACCCCGGCACCCCGGGCATCCTCCGCATGgtgcgtgccaccctccccttctctctcactccctgcggctctctctcccttcaccttcctcccgacgagtgcgcacggtccgctaacaagctccgggctg...

Basic information

species Zea mays
transcript GRMZM5G870572_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G870572_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os08g25060.1 (Oryza sativa), 5'ss of exon 1
AGCCACCGCGGCGGCGGTTGCAGCGATGGGGTCCATGACGATCGGTGCCAAGTACAAGACCACGATCAAGGACCCCGGCACCCCGGGCATCCTCCGCATGgtgcgt-gccaccctccccttctctctcactccctgcggctctctc---tcccttcaccttcctcccgacgagtgcgcacggtccgctaacaagctccgggctg
 |     |||  || ||   | ||||||||||||||||||||||| |||||||||||||||||| ||||||||||||||||| | ||| |||| |||||||||||| || | || |||  | |  ||| ||||||    ||||| |   |  | || |||  |||||  |   | ||   |||| | |   || |   | |   
CGTGGAGGCGTGGGGGGCGACGGCGATGGGGTCCATGACGATCGGCGCCAAGTACAAGACCACGCTCAAGGACCCCGGCACCACCGGCGTCCTGCGCATGgtgcgtcgcgatcccccctctgttcctccctccctctctctctcccgcatagcgtcgcctctctccctccagctccgattggtcgggtt-taacccttgcg---
















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|211184536|gb|FL153191.1|FL153191
EST:     AGTACAAGACCACGATCAAGGACCCCGGCACCCCGGGCATCCTCCGCATG                         AACGGTGATAGGTTCACCTTCACCCCTAATGATCCACGATCGGCAATGAAG
genomic: AGTACAAGACCACGATCAAGGACCCCGGCACCCCGGGCATCCTCCGCATGgtgcgtgcca ... ctaattacagAACGGTGATAGGTTCACCTTCACCCCTAATGATCCACGATCGGCAATGAAG
EST: gi|211184539|gb|FL153194.1|FL153194
EST:     AGTACAAGACCACGATCAAGGACCCCGGCACCCCGGGCATCCTCCGCATG                         AACGGTGATAGGTTCACCTTCACCCCTAATGATCCACGATCGGCAATGAAG
genomic: AGTACAAGACCACGATCAAGGACCCCGGCACCCCGGGCATCCTCCGCATGgtgcgtgcca ... ctaattacagAACGGTGATAGGTTCACCTTCACCCCTAATGATCCACGATCGGCAATGAAG
EST: gi|211184530|gb|FL153185.1|FL153185
EST:     AGTACAAGACCACGATCAAGGACCCCGGCACCCCGGGCATCCTCCGCATG                         AACGGTGATAGGTTCACCTTCACCCCTAATGATCCACGATCGGCAATGAAG
genomic: AGTACAAGACCACGATCAAGGACCCCGGCACCCCGGGCATCCTCCGCATGgtgcgtgcca ... ctaattacagAACGGTGATAGGTTCACCTTCACCCCTAATGATCCACGATCGGCAATGAAG
EST: gi|211184534|gb|FL153189.1|FL153189
EST:     AGTACAAGACCACGATCAAGGACCCCGGCACCCCGGGCATCCTCCGCATG                         AACGGTGATAGGTTCACCTTCACCCCTAATGATCCACGATCGGCAATGAAG
genomic: AGTACAAGACCACGATCAAGGACCCCGGCACCCCGGGCATCCTCCGCATGgtgcgtgcca ... ctaattacagAACGGTGATAGGTTCACCTTCACCCCTAATGATCCACGATCGGCAATGAAG
EST: gi|211184537|gb|FL153192.1|FL153192
EST:     AGTACAAGACCACGATCNAGGACCCCGGCACCCCGGGCATCCTCCGCATG                         AACGGTGATAGGTTCACCTTCACCCC-AATGATCCACGATCGGCAATGAAG
genomic: AGTACAAGACCACGATCAAGGACCCCGGCACCCCGGGCATCCTCCGCATGgtgcgtgcca ... ctaattacagAACGGTGATAGGTTCACCTTCACCCCTAATGATCCACGATCGGCAATGAAG
EST: gi|148959670|gb|EC905590.2|EC905590
EST:     AGTACAAGACCACGATCAAGGACCCCGGCACCCCGGGCATCCTCCGCATG                         AACGGTGATAGGTTCACCTTCACCCCTAATGATCCACGATCGGCAATGAAG
genomic: AGTACAAGACCACGATCAAGGACCCCGGCACCCCGGGCATCCTCCGCATGgtgcgtgcca ... ctaattacagAACGGTGATAGGTTCACCTTCACCCCTAATGATCCACGATCGGCAATGAAG
EST: gi|211184535|gb|FL153190.1|FL153190
EST:     AGTACAAGACCACGATCAAGGACCCCGGCACCCCGGGCATCCTCCGCATG                         AACGGTGATAGGTTCACCTTCACCCCTAATGATCCACGATCGGCAATGAAG
genomic: AGTACAAGACCACGATCAAGGACCCCGGCACCCCGGGCATCCTCCGCATGgtgcgtgcca ... ctaattacagAACGGTGATAGGTTCACCTTCACCCCTAATGATCCACGATCGGCAATGAAG
EST: gi|211184538|gb|FL153193.1|FL153193
EST:     AGTACAAGACCACGATCAAGGACCCCGGCACCCCGGGCATCCTCCGCATG                         AACGGTGATAGGTTCACCTTCACCCCTAATGATCCACGATCGGCAATGAAG
genomic: AGTACAAGACCACGATCAAGGACCCCGGCACCCCGGGCATCCTCCGCATGgtgcgtgcca ... ctaattacagAACGGTGATAGGTTCACCTTCACCCCTAATGATCCACGATCGGCAATGAAG
EST: gi|89756532|gb|DY686536.1|DY686536
EST:     AGTACAAGACCACGATCAAGGACCCCGGCACCCCGGGCATCCTCCGCATG                         AACGGTGATAGGTTCACCTTCACCCCTAATGATCCACGATCGGCAATGAAG
genomic: AGTACAAGACCACGATCAAGGACCCCGGCACCCCGGGCATCCTCCGCATGgtgcgtgcca ... ctaattacagAACGGTGATAGGTTCACCTTCACCCCTAATGATCCACGATCGGCAATGAAG
EST: gi|211184531|gb|FL153186.1|FL153186
EST:     AGTACAAGACCACGATCAAGGACCCCGGCACCCCGGGCATCCTCCGCATG                         AACGGTGATAGGTTCACCTTCACCCCTAATGATCCACGATCGGCAATGAAG
genomic: AGTACAAGACCACGATCAAGGACCCCGGCACCCCGGGCATCCTCCGCATGgtgcgtgcca ... ctaattacagAACGGTGATAGGTTCACCTTCACCCCTAATGATCCACGATCGGCAATGAAG
EST: gi|211184529|gb|FL153184.1|FL153184
EST:     AGTACAAGACCACGATCAAGGACCCCGGCACCCCGGGCATCCTCCGCATG                         AACGGTGATAGGTTCACCTTCACCCCTAATGATCCACGATCGGCAATGAAG
genomic: AGTACAAGACCACGATCAAGGACCCCGGCACCCCGGGCATCCTCCGCATGgtgcgtgcca ... ctaattacagAACGGTGATAGGTTCACCTTCACCCCTAATGATCCACGATCGGCAATGAAG

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: 32

AGCCACCGCGGCGGCGGTTGCAGCGATGGGGTCCATGACGATCGGTGCCAAGTACAAGACCACGATCAAGGACCCCGGCACCCCGGGCATCCTCCGCATGgtgcgtgcca ... ctaattacagAACGGTGATAGGTTCACCTTCACCCCTAATGATCCACGATCGGCAATGAAGTTCAATGTTGATTTCCGAACCATCAAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 28

AGCCACCGCGGCGGCGGTTGCAGCGATGGGGTCCATGACGATCGGTGCCAAGTACAAGACCACGATCAAGGACCCCGGCACCCCGGGCATCCTCCGCATGgtgcgtgcca ... ctaattacagAACGGTGATAGGTTCACCTTCACCCCTAATGATCCACGATCGGCAATGAAGTTCAATGTTGATTTCCGAACCATCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 59

AGCCACCGCGGCGGCGGTTGCAGCGATGGGGTCCATGACGATCGGTGCCAAGTACAAGACCACGATCAAGGACCCCGGCACCCCGGGCATCCTCCGCATGgtgcgtgcca ... ctaattacagAACGGTGATAGGTTCACCTTCACCCCTAATGATCCACGATCGGCAATGAAGTTCAATGTTGATTTCCGAACCATCAAAG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 26

AGCCACCGCGGCGGCGGTTGCAGCGATGGGGTCCATGACGATCGGTGCCAAGTACAAGACCACGATCAAGGACCCCGGCACCCCGGGCATCCTCCGCATGgtgcgtgcca ... ctaattacagAACGGTGATAGGTTCACCTTCACCCCTAATGATCCACGATCGGCAATGAAGTTCAATGTTGATTTCCGAACCATCAAAG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCCACCGCGGCGGCGGTTGCAGCGATGGGGTCCATGACGATCGGTGCCAAGTACAAGACCACGATCAAGGACCCCGGCACCCCGGGCATCCTCCGCATGgtgcgtgccaccctccccttctctctcactccctgcggctctctctcccttcaccttcctcccgacgagtgcgcacggtccgctaacaagctccgggctg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttcctcc