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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaacaactcacgatttctcagtttcttctctaccctttgatctttatttgcaagtggtcgcatgtagacttgatttgctagttgttactgcaataatgatgcatttgttactgaaaccttttgtcatcatttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTGGATAACCAAGAAGGAGCAAACCAGCATCAGGTCGTGCACGCCAATGATA

Basic information

species Zea mays
transcript GRMZM2G067546_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G067546_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os03g21720.1 (Oryza sativa), 3'ss of exon 11
gtaaaacaactcacgatttctcagtttcttctctaccctttgatctttatttgcaagtggtcgcatgtagacttgatttgctagttgttactgcaataatgatgcatttgttactgaaaccttttgtcatcatttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTGGATAACCAAGAAGGAGCAAACCAGCATCAGGTCGTGCACGCCAATGATA
|||||||| || || |    | | || ||     ||  |||  |  | ||       ||| | ||||| |    || |||| |  || |||   |||   | |||       | | || |  |           ||| ||||| ||||||||||| ||||| || || |||||||| |||||||||||| ||||||||||||||| ||| ||||| ||||| |||| ||| ||   |||| 
gtaaaacatct-accaccctttatttcctc----actttttagttatcat------atggccacatgtgg----gacttgc-acctgatac-ataattgagttgctaactggattcaatctgtgccatgatgcctcatcagAGCTACATGGATTCGGAGATTCGCGCGATCATGGCCCAGTACATGCCTTTGGATAACCAAGAAGCAGCTAACCAACATCATGTCGCGCATGCTGGTGATG
















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|24764971|gb|CA400147.1|CA400147
EST:     TTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGG                         AGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
genomic: TTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGGgtaaaacaac ... atttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
EST: gi|211108137|gb|FL478050.1|FL478050
EST:     TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGG                         AGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
genomic: TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGGgtaaaacaac ... atttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
EST: gi|148949555|gb|EC895022.2|EC895022
EST:     TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGG                         AGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
genomic: TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGGgtaaaacaac ... atttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
EST: gi|6828165|gb|AW331808.1|AW331808
EST:     TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGG                         AGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
genomic: TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGGgtaaaacaac ... atttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
EST: gi|67015635|gb|CO444384.1|CO444384
EST:     GTTTTTGCCCGGGGTTG-AGCATACGCTGTGTACAAATACAGGCTGCNNG                         A-TTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCT
genomic: GTTTTTGCC-GGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCG-Ggtaaaacaac ... atttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCT
EST: gi|6227124|gb|AW155653.1|AW155653
EST:     TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGG                         AGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
genomic: TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGGgtaaaacaac ... atttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
EST: gi|148962555|gb|EE013431.2|EE013431
EST:     TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGG                         AGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
genomic: TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGGgtaaaacaac ... atttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
EST: gi|60396640|gb|DN229508.1|DN229508
EST:     TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGG                         AGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
genomic: TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGGgtaaaacaac ... atttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
EST: gi|60340337|gb|DN207310.1|DN207310
EST:     TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGG                         AGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTTTG
genomic: TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGGgtaaaacaac ... atttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
EST: gi|30032111|gb|CB833962.1|CB833962
EST:     TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGG                         AGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
genomic: TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGGgtaaaacaac ... atttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
EST: gi|60401526|gb|DN234333.1|DN234333
EST:     TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGG                         AGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
genomic: TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGGgtaaaacaac ... atttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
EST: gi|148966624|gb|EE017666.2|EE017666
EST:     TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGG                         AGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
genomic: TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGGgtaaaacaac ... atttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
EST: gi|37374458|gb|CF623588.1|CF623588
EST:     GAGCATACGCTGTGTACAAATACAGGCTGCGG                         AGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
genomic: GAGCATACGCTGTGTACAAATACAGGCTGCGGgtaaaacaac ... atttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
EST: gi|67019769|gb|CO448518.1|CO448518
EST:     TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGG                         AGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
genomic: TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGGgtaaaacaac ... atttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
EST: gi|211348715|gb|FL063226.1|FL063226
EST:     TTGTTTTTGCCGGGGTTGGAGCATACGCTATGTACAAATACAGGCTGCGG                         AGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
genomic: TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGGgtaaaacaac ... atttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
EST: gi|7216544|gb|AW562666.1|AW562666
EST:     TTG-TTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGG                         AGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTTTG
genomic: TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGGgtaaaacaac ... atttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
EST: gi|149099685|gb|EE185734.2|EE185734
EST:     TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGG                         AGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
genomic: TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGGgtaaaacaac ... atttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
EST: gi|67013253|gb|CO442002.1|CO442002
EST:     TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGG                         AGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
genomic: TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGGgtaaaacaac ... atttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
EST: gi|29544790|gb|CB605398.1|CB605398
EST:     TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGG                         AGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
genomic: TTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGGgtaaaacaac ... atttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
EST: gi|62525925|gb|DN828573.1|DN828573
EST:     GGAGCATACGCTGTGTACAAATACAGGCTGCGG                         AGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG
genomic: GGAGCATACGCTGTGTACAAATACAGGCTGCGGgtaaaacaac ... atttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTG

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: 48 (upstream exon), 43 (downstream exon)
Score: 60

AACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTTTCTTTGGACTTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGGgtaaaacaac ... atttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTGGATAACCAAGAAGGAGCAAACCAGCATCAGGTCGTGCACGCCAATGATA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 307

AACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTTTCTTTGGACTTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGGgtaaaacaac ... atttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTGGATAACCAAGAAGGAGCAAACCAGCATCAGGTCGTGCACGCCAATGATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 298

AACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTTTCTTTGGACTTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGGgtaaaacaac ... atttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTGGATAACCAAGAAGGAGCAAACCAGCATCAGGTCGTGCACGCCAATGATA


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 101

AACTGCCACTACTGTTGGCTGGAGCTTCCTCTGGGTTATTTTCTTTGGACTTGTTTTTGCCGGGGTTGGAGCATACGCTGTGTACAAATACAGGCTGCGGgtaaaacaac ... atttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTGGATAACCAAGAAGGAGCAAACCAGCATCAGGTCGTGCACGCCAATGATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttactgcaataatgatgcatttgttactgaaaccttttgtcatcatttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTGGATAACCAAGAAGGAGCAAACCAGCATCAGGTCGTGCACGCCAATGATA
                                           tcatttc  CT-rich tract
        aataatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaacaactcacgatttctcagtttcttctctaccctttgatctttatttgcaagtggtcgcatgtagacttgatttgctagttgttactgcaataatgatgcatttgttactgaaaccttttgtcatcatttcaccagAGTTACATGGATTCAGAGATCCGTGCCATCATGGCTCAGTACATGCCTCTGGATAACCAAGAAGGAGCAAACCAGCATCAGGTCGTGCACGCCAATGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA