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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGCCCAAGGGCTACTACGTGCAGGTGGACACCGGCAGCGATATCCTCTGGGTCAACTGCATCCGCTGCGATGGCTGCCCCACCAGAAGCGGACTTGGGgtactgctccatctgaccatctccatggccaggccacaccaggccatgcgcgatgctcccatgccatgcttgtccctatggtccttgcctgcttggtgtgatgatttttgtcgtgaagaatcgtccttccctgcgcgttggtttggttgcag

Basic information

species Zea mays
transcript GRMZM2G411333_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G411333_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g27360.2 (Oryza sativa), 5'ss of exon 2
GCCGCCCAAGGGCTACTACGTGCAGGTGGACACCGGCAGCGATATCCTCTGGGTCAACTGCATCCGCTGCGATGGCTGCCCCACCAGAAGCGGACTTGGGgtactgctccatctgaccatctccatggccaggccacaccaggccatgcgcgatgctcccatgccatgcttgtccctatggtccttgcctgcttggtgtgatgatttttgtcgtgaagaatcgtccttccctgcgcgttggtttggttgcag
|||| | ||| ||||||||||||||||||||||||||||||| |||||||||||||||||| ||  |||||| ||||||||   ||  |||   || ||||| |    | | ||||||   |||    ||      | ||    | |||    | | ||| |      || || || |   |   ||  || ||  || |  || |||||  |                                       
GCCGGCGAAGCGCTACTACGTGCAGGTGGACACCGGCAGCGACATCCTCTGGGTCAACTGCGTCTCCTGCGACGGCTGCCCGCGCAAGAGCAACCTCGGGgtgcgatacta-ctgacc---tccgattcctccttcctcc----cctgcagattccccccct------ctcgtgcccagattggatgtttgatt--tggggggagttttgcag---------------------------------------
















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|71443428|gb|DR824478.1|DR824478
EST:     GGGTCAACTGCATCCGCTGCGATGGCTGCCCCACCAGAAGCGGACTTGGG                         ATAGAGCTGACGCAGTACGATCCGGCTGGGAGCGGGACCACGGTGGGGTGC
genomic: GGGTCAACTGCATCCGCTGCGATGGCTGCCCCACCAGAAGCGGACTTGGGgtactgctcc ... ttggttgcagATAGAGCTGACGCAGTACGATCCGGCTGGGAGCGGGACCACGGTGGGGTGC
EST: gi|71329431|gb|DR801432.1|DR801432
EST:     GGGTCAACTGCATCCGCTGCGATGGCTGCCCCACCAGAAGCGGACTTGGG                         ATAGAGCTGACGCAGTACGATCCGGCTGGGAGCGGGACCACGGTGGGGTGC
genomic: GGGTCAACTGCATCCGCTGCGATGGCTGCCCCACCAGAAGCGGACTTGGGgtactgctcc ... ttggttgcagATAGAGCTGACGCAGTACGATCCGGCTGGGAGCGGGACCACGGTGGGGTGC
EST: gi|94472394|gb|EB701352.1|EB701352
EST:     GGGTCAACTGCATCCGCTGCGATGGCTGCCCCACCAGAAGCGGACTTGGG                         ATAGAGCTGACGCAGTACGATCCGGCTGGGAGCGGGACCACGGTGGGGTGC
genomic: GGGTCAACTGCATCCGCTGCGATGGCTGCCCCACCAGAAGCGGACTTGGGgtactgctcc ... ttggttgcagATAGAGCTGACGCAGTACGATCCGGCTGGGAGCGGGACCACGGTGGGGTGC
EST: gi|148946390|gb|EC891698.2|EC891698
EST:     GGGTCAACTGCATCCGCTGCGATGGCTGCCCCACCAGAAGCGGACTTGGG                         ATAGAGCTGACGCAGTACGATCCGGCTGGGAGCGGGACCACGGTGGGGTGC
genomic: GGGTCAACTGCATCCGCTGCGATGGCTGCCCCACCAGAAGCGGACTTGGGgtactgctcc ... ttggttgcagATAGAGCTGACGCAGTACGATCCGGCTGGGAGCGGGACCACGGTGGGGTGC
EST: gi|71309094|gb|DR790817.1|DR790817
EST:     GGGTCAACTGCATCCGCTGCGATGGCTGCCCCACCAGAAGCGGACTTGGG                         ATAGAGCTGACGCAGTACGATCCGGCTGGGAGCGGGACCACGGTGGGGTGC
genomic: GGGTCAACTGCATCCGCTGCGATGGCTGCCCCACCAGAAGCGGACTTGGGgtactgctcc ... ttggttgcagATAGAGCTGACGCAGTACGATCCGGCTGGGAGCGGGACCACGGTGGGGTGC
EST: gi|31356527|gb|CD440884.1|CD440884
EST:     GGGTCAACTGCATCCGCTGCGACGGCTGCCCCACCAGGAGCGGCCTCGGG                         ATAGAGCTGACGCAGTACGATCCGGCTGGGAGCGGGACCACGGTGGGGTGC
genomic: GGGTCAACTGCATCCGCTGCGATGGCTGCCCCACCAGAAGCGGACTTGGGgtactgctcc ... ttggttgcagATAGAGCTGACGCAGTACGATCCGGCTGGGAGCGGGACCACGGTGGGGTGC
EST: gi|71438608|gb|DR819658.1|DR819658
EST:     GGGTCAACTGCATCCGCTGCGATGGCTGCCCCACCAGAAGCGGACTTGGG                         ATAGAGCTGACGCAGTACGATCCGGCTGGGAGCGGGACCACGGTGGGGTGC
genomic: GGGTCAACTGCATCCGCTGCGATGGCTGCCCCACCAGAAGCGGACTTGGGgtactgctcc ... ttggttgcagATAGAGCTGACGCAGTACGATCCGGCTGGGAGCGGGACCACGGTGGGGTGC
EST: gi|148962846|gb|EE013768.2|EE013768
EST:     GGGTCAACTGCATCCGCTGCGATGGCTGCCCCACCAGAAGCGGACTTGGG                         ATAGAGCTGACGCAGTACGATCCGGCTGGGAGCGGGACCACGGTGGGGTGC
genomic: GGGTCAACTGCATCCGCTGCGATGGCTGCCCCACCAGAAGCGGACTTGGGgtactgctcc ... ttggttgcagATAGAGCTGACGCAGTACGATCCGGCTGGGAGCGGGACCACGGTGGGGTGC
EST: gi|50335617|gb|CO530743.1|CO530743
EST:     GGGTCAACTGCATCCGCTGCGATGGCTGCCCCACCAGAAGCGGACTTGGG                         ATAGAGCTGACGCAGTACGATCCGGCTGGGAGCGGGACCACGGTGGGGTGC
genomic: GGGTCAACTGCATCCGCTGCGATGGCTGCCCCACCAGAAGCGGACTTGGGgtactgctcc ... ttggttgcagATAGAGCTGACGCAGTACGATCCGGCTGGGAGCGGGACCACGGTGGGGTGC
EST: gi|149010274|gb|EE042101.2|EE042101
EST:     GGGTCAACTGCATCCGCTGCGATGGCTGCCCCACCAGAAGCGGACTTGGG                         ATAGAGCTGACGCAGTACGATCCGGCTGGGAGCGGGACCACGGTGGGGTGC
genomic: GGGTCAACTGCATCCGCTGCGATGGCTGCCCCACCAGAAGCGGACTTGGGgtactgctcc ... ttggttgcagATAGAGCTGACGCAGTACGATCCGGCTGGGAGCGGGACCACGGTGGGGTGC
EST: gi|91048431|gb|EB158849.1|EB158849
EST:     GGGTCAACTGCATCCGCTGCGATGGCTGCCCCACCAGAAGCGGACTTGGG                         ATAGAGCTGACGCAGTACGATCCGGCTGGGAGCGGGACCACGGTGGGGTGC
genomic: GGGTCAACTGCATCCGCTGCGATGGCTGCCCCACCAGAAGCGGACTTGGGgtactgctcc ... ttggttgcagATAGAGCTGACGCAGTACGATCCGGCTGGGAGCGGGACCACGGTGGGGTGC

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), 45 (downstream exon)
Score: 21

GCCGCCCAAGGGCTACTACGTGCAGGTGGACACCGGCAGCGATATCCTCTGGGTCAACTGCATCCGCTGCGATGGCTGCCCCACCAGAAGCGGACTTGGGgtactgctcc ... ttggttgcagATAGAGCTGACGCAGTACGATCCGGCTGGGAGCGGGACCACGGTGGGGTGCGAGCAGGAGTTCTGCGTTGCCAACAGCGCGGGCGGCGTGCCCCCCACGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 81

GCCGCCCAAGGGCTACTACGTGCAGGTGGACACCGGCAGCGATATCCTCTGGGTCAACTGCATCCGCTGCGATGGCTGCCCCACCAGAAGCGGACTTGGGgtactgctcc ... ttggttgcagATAGAGCTGACGCAGTACGATCCGGCTGGGAGCGGGACCACGGTGGGGTGCGAGCAGGAGTTCTGCGTTGCCAACAGCGCGGGCGGCGTGCCCCCCACGT


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 98

GCCGCCCAAGGGCTACTACGTGCAGGTGGACACCGGCAGCGATATCCTCTGGGTCAACTGCATCCGCTGCGATGGCTGCCCCACCAGAAGCGGACTTGGGgtactgctcc ... ttggttgcagATAGAGCTGACGCAGTACGATCCGGCTGGGAGCGGGACCACGGTGGGGTGCGAGCAGGAGTTCTGCGTTGCCAACAGCGCGGGCGGCGTGCCCCCCACGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 64

GCCGCCCAAGGGCTACTACGTGCAGGTGGACACCGGCAGCGATATCCTCTGGGTCAACTGCATCCGCTGCGATGGCTGCCCCACCAGAAGCGGACTTGGGgtactgctcc ... ttggttgcagATAGAGCTGACGCAGTACGATCCGGCTGGGAGCGGGACCACGGTGGGGTGCGAGCAGGAGTTCTGCGTTGCCAACAGCGCGGGCGGCGTGCCCCCCACGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCGCCCAAGGGCTACTACGTGCAGGTGGACACCGGCAGCGATATCCTCTGGGTCAACTGCATCCGCTGCGATGGCTGCCCCACCAGAAGCGGACTTGGGgtactgctccatctgaccatctccatggccaggccacaccaggccatgcgcgatgctcccatgccatgcttgtccctatggtccttgcctgcttggtgtgatgatttttgtcgtgaagaatcgtccttccctgcgcgttggtttggttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC