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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAGgtagtgctttctcatacctgctgcggccagcttcacacagatttggttgctcattttatgagtgtctcaatcacattgtactcaaacttgattactgaatttcacataaaaaactttcctaatcag

Basic information

species Zea mays
transcript GRMZM2G123624_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G123624_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os10g36870.1 (Oryza sativa), 5'ss of exon 9
GCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAGgtagtgctttctcatacctgctgcggccagcttcacacagatttggttgctcattttatgagtgtctcaatcacattgtactcaaacttgattac--tgaatttcacataaaaaactttcctaatcag
|| ||||| || ||||| || ||||| || |||||||||||||| ||||||||||||| ||||| ||||| |||||| || | || | || || | | | ||| || | ||| || | |||| |||| ||| ||| | || || | | ||| | | ||||||
GCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCTGGTGACTATATAGTTGTCCGGAAGgtacggccctatctt-cccattg-gacatgtttctaacca---taaacatatctttgctggactt----------ttgtgggcaaagttggctacactaaacttgtgttcattaacctgctcaatcag
















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|60398124|gb|DN230940.1|DN230940
EST:     GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
genomic: GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
EST: gi|28985206|gb|BQ539380.2|BQ539380
EST:     GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
genomic: GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
EST: gi|78545157|gb|DV622655.1|DV622655
EST:     GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
genomic: GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
EST: gi|32919380|gb|CF024192.1|CF024192
EST:     GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
genomic: GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
EST: gi|71768413|gb|DR966350.1|DR966350
EST:     GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
genomic: GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
EST: gi|60341099|gb|DN208072.1|DN208072
EST:     GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
genomic: GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
EST: gi|74239023|gb|DT646937.1|DT646937
EST:     GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
genomic: GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
EST: gi|211106266|gb|FL250478.1|FL250478
EST:     GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
genomic: GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
EST: gi|4610060|gb|AI600899.1|AI600899
EST:     ACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
genomic: ACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
EST: gi|6021751|gb|AW066679.1|AW066679
EST:     GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
genomic: GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
EST: gi|78074542|gb|DV502976.1|DV502976
EST:     GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
genomic: GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
EST: gi|76019273|gb|DT946443.1|DT946443
EST:     GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
genomic: GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
EST: gi|16916604|gb|BM072914.1|BM072914
EST:     GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
genomic: GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
EST: gi|60358710|gb|DN225683.1|DN225683
EST:     GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
genomic: GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
EST: gi|166483159|gb|EG165296.1|EG165296
EST:     GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGC
genomic: GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGC
EST: gi|211409238|gb|FL441029.1|FL441029
EST:     GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
genomic: GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
EST: gi|71765023|gb|DR962960.1|DR962960
EST:     GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
genomic: GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
EST: gi|78026827|gb|DV495214.1|DV495214
EST:     GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
genomic: GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
EST: gi|71756340|gb|DR954277.1|DR954277
EST:     GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
genomic: GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
EST: gi|149085094|gb|EE174601.2|EE174601
EST:     GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
genomic: GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
EST: gi|71328409|gb|DR800841.1|DR800841
EST:     GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
genomic: GCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
EST: gi|4624320|gb|AI615153.1|AI615153
EST:     ACTACATAGTGGTCCGAAAG                         GTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG
genomic: ACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGG

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), 48 (downstream exon)
Score: 201

GCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGGTTCCCCTACGACTACATCGAGAAACGAGAGCGTGTGCTTGCAAGTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 111

GCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGGTTCCCCTACGACTACATCGAGAAACGAGAGCGTGTGCTTGCAAGTAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 93

GCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGGTTCCCCTACGACTACATCGAGAAACGAGAGCGTGTGCTTGCAAGTAAAG


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 65

GCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAGgtagtgcttt ... tcctaatcagGTGTCGAACAATGGATGGGCCGAAGGTGAATGCAGGGGGAGAGCTGGCTGGTTCCCCTACGACTACATCGAGAAACGAGAGCGTGTGCTTGCAAGTAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAATCCAATCATATCGAGCAGAGAGCGACACTGAGCTCAACCTTTCAGCTGGTGACTACATAGTGGTCCGAAAGgtagtgctttctcatacctgctgcggccagcttcacacagatttggttgctcattttatgagtgtctcaatcacattgtactcaaacttgattactgaatttcacataaaaaactttcctaatcag

- - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - CAGCTG