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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaaaaaaacctgtatatgttaataaggtgatcggaatagtccaggatgtaattcaggcaattctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATG

Basic information

species Zea mays
transcript GRMZM2G134582_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G320497_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g12800.1 (Oryza sativa), 3'ss of exon 3
gtatgaaaaaaacctgtatatgttaataaggtgatcggaatagtccaggatgtaattcaggcaa--ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATG
|| |||  ||||||   |  | | |||   |  |    | | |  ||| || | |||  | ||   ||| ||  || | ||| | || |||||||||||||||||||||||||| |||||||| |||||| ||||||
gtttgagcaaaacc---acctctgaattttggtac---atttgcacagaatctgatttggacacgtttcctttcagGTCCCTATTCTAGAGACTCCTGATGGTCCTGTTTTTGAAAGCAATGCGATTGCACGATATG
















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|211419497|gb|FK986932.1|FK986932
EST:     GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAG                         ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
genomic: GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAGgtatgaaaaa ... ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
EST: gi|67025845|gb|CO454594.1|CO454594
EST:     GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAG                         ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
genomic: GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAGgtatgaaaaa ... ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
EST: gi|211299931|gb|FL223399.1|FL223399
EST:     GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAG                         ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
genomic: GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAGgtatgaaaaa ... ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
EST: gi|211419502|gb|FK986937.1|FK986937
EST:     GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAG                         ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
genomic: GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAGgtatgaaaaa ... ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
EST: gi|211269909|gb|FK986924.1|FK986924
EST:     GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAG                         ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
genomic: GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAGgtatgaaaaa ... ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
EST: gi|17930924|gb|BM267884.1|BM267884
EST:     GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAG                         ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
genomic: GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAGgtatgaaaaa ... ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
EST: gi|15053873|gb|BI359418.1|BI359418
EST:     GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAG                         ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
genomic: GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAGgtatgaaaaa ... ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
EST: gi|211269911|gb|FK986926.1|FK986926
EST:     GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAG                         ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
genomic: GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAGgtatgaaaaa ... ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
EST: gi|31354444|gb|CD438801.1|CD438801
EST:     GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAG                         ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
genomic: GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAGgtatgaaaaa ... ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
EST: gi|15209068|gb|BI430952.1|BI430952
EST:     GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAG                         ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
genomic: GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAGgtatgaaaaa ... ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
EST: gi|50333934|gb|CO529060.1|CO529060
EST:     GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAG                         ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
genomic: GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAGgtatgaaaaa ... ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
EST: gi|211269910|gb|FK986925.1|FK986925
EST:     GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAG                         ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
genomic: GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAGgtatgaaaaa ... ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
EST: gi|211419500|gb|FK986935.1|FK986935
EST:     GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAG                         ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
genomic: GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAGgtatgaaaaa ... ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
EST: gi|21891605|gb|BQ744818.1|BQ744818
EST:     GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAG                         ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
genomic: GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAGgtatgaaaaa ... ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
EST: gi|211244386|gb|FL238837.1|FL238837
EST:     GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAG                         ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
genomic: GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAGgtatgaaaaa ... ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
EST: gi|211269915|gb|FK986930.1|FK986930
EST:     GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAG                         ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTYGAGAGCAATGCAATT
genomic: GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAGgtatgaaaaa ... ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
EST: gi|60398445|gb|DN231261.1|DN231261
EST:     GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAG                         ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
genomic: GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAGgtatgaaaaa ... ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
EST: gi|211512831|gb|FL354907.1|FL354907
EST:     GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAG                         ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
genomic: GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAGgtatgaaaaa ... ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
EST: gi|31354453|gb|CD438810.1|CD438810
EST:     GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAG                         ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
genomic: GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAGgtatgaaaaa ... ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
EST: gi|67020169|gb|CO448918.1|CO448918
EST:     GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAG                         ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
genomic: GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAGgtatgaaaaa ... ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
EST: gi|211269908|gb|FK986923.1|FK986923
EST:     GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAG                         ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
genomic: GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAGgtatgaaaaa ... ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
EST: gi|60399613|gb|DN232423.1|DN232423
EST:     GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAG                         ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
genomic: GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAGgtatgaaaaa ... ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
EST: gi|6020992|gb|AW065920.1|AW065920
EST:     TTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAG                         ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
genomic: GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAGgtatgaaaaa ... ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
EST: gi|14529440|gb|BI096573.1|BI096573
EST:     GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAG                         ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT
genomic: GTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAGgtatgaaaaa ... ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATT

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: 237

CGCAGAATACAGCGGTGTCAAGGTTGAGTTGGTGAAGGACTTTCAAATGGGTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAGgtatgaaaaa ... ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 226

CGCAGAATACAGCGGTGTCAAGGTTGAGTTGGTGAAGGACTTTCAAATGGGTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAGgtatgaaaaa ... ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 206

CGCAGAATACAGCGGTGTCAAGGTTGAGTTGGTGAAGGACTTTCAAATGGGTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAGgtatgaaaaa ... ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 260

CGCAGAATACAGCGGTGTCAAGGTTGAGTTGGTGAAGGACTTTCAAATGGGTGTCTCCAACAAAACTCCAGAGTTCCTCAAGATGAACCCTATTGGGAAGgtatgaaaaa ... ttctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttaataaggtgatcggaatagtccaggatgtaattcaggcaattctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATG
 tgttaat  putative branch site (score: 260)
                                             ttctttgt  putative PPT
                              atgtaatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaaaaaaacctgtatatgttaataaggtgatcggaatagtccaggatgtaattcaggcaattctttgtagATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA