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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGAAGATCCCTTCCATCCATGGGTTCACGACGGGCCTGAAGCTTGAACAGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaatttctatctaaccataggctcacatgttttcttcttcttgttcctcatcaagagcaggggaaacaaaaaaacttcag

Basic information

species Zea mays
transcript GRMZM2G044629_T01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044629_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os04g52370.2 (Oryza sativa), 5'ss of exon 13
GAAGAAGATCCCTTCCATCCATGGGTTCACGACGGGCCTGAAGCTTGAACAGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaatttctatctaaccataggctcaca-tgtttt---cttcttcttgt---tcctcatcaagagcaggggaaacaaaaaaacttcag---------------
|||||||||||||||||||||||||| | | | |||| ||||||||||||||| |||||||||||| ||||  |||||||| ||||| |||||||| |||||   | ||   |     | ||   || | |   || |     || |  |||   |  |  | | ||    | |||||  |      |                  
GAAGAAGATCCCTTCCATCCATGGGTACGCAATGGGCTTGAAGCTTGAACAGTATATATTCGACGCGTTCAGTTACTCCCCATCCACAGCACTTTTTGAGgttcaacttctcagtcgcctatgctcttataacattctagatgtcatgctgtgtctttttgttatgattttgagaaactcatcggtatacatatctgaaaattcag
















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|149100895|gb|EE186990.2|EE186990
EST:     AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|71429564|gb|DR810614.1|DR810614
EST:     AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|166514172|gb|EG308864.1|EG308864
EST:     CGGCACTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: CGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|211094109|gb|FL460556.1|FL460556
EST:     NGTTTATATTCGACGCTTTCACATACTGCCCGTCCACGGCACTTTTGGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: -GTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|166625031|gb|EG168092.1|EG168092
EST:     GTCCACGGCACTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: GTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|37378055|gb|CF625683.1|CF625683
EST:     AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|211406602|gb|FL094198.1|FL094198
EST:     AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|78115802|gb|DV534190.1|DV534190
EST:     AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|149014876|gb|EE044587.2|EE044587
EST:     AGTTTATATTGGACGCCTTCACATACTCCCCGTCCACGGCACTTTTGGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|94477176|gb|EB706134.1|EB706134
EST:     AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|37397991|gb|CF636304.1|CF636304
EST:     AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|211119105|gb|FL479440.1|FL479440
EST:     AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|91052248|gb|EB162666.1|EB162666
EST:     AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|24769018|gb|CA404147.1|CA404147
EST:     AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTTGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|71772484|gb|DR970416.1|DR970416
EST:     AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|16926697|gb|BM079765.1|BM079765
EST:     AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|14244148|gb|BG841843.2|BG841843
EST:     AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG

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), 46 (downstream exon)
Score: 78

GAAGAAGATCCCTTCCATCCATGGGTTCACGACGGGCCTGAAGCTTGAACAGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACGTATGACACCCCTGATAGCGCGAAGCTCATGCTGCTCCGCCTCCACAGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 201

GAAGAAGATCCCTTCCATCCATGGGTTCACGACGGGCCTGAAGCTTGAACAGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACGTATGACACCCCTGATAGCGCGAAGCTCATGCTGCTCCGCCTCCACAGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 310

GAAGAAGATCCCTTCCATCCATGGGTTCACGACGGGCCTGAAGCTTGAACAGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACGTATGACACCCCTGATAGCGCGAAGCTCATGCTGCTCCGCCTCCACAGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 232

GAAGAAGATCCCTTCCATCCATGGGTTCACGACGGGCCTGAAGCTTGAACAGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACGTATGACACCCCTGATAGCGCGAAGCTCATGCTGCTCCGCCTCCACAGCA