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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttaacctcatcaacaattcagatacacgatggtgctcccctgataccggatgctgcaagttaaaggatgcgtgcatatatactcatactgaatgtgttctttgtggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATGACATGGATACGTCCTCTGCAGACGCGGCTTACAACACGACCAACACATA

Basic information

species Zea mays
transcript GRMZM2G351582_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G351582_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os08g36774.1 (Oryza sativa), 3'ss of exon 15
gtaagttaacctcatcaacaattcagatacacgatggtgctcccctgataccggatgctgcaagttaaaggatgcgtgcatatatactcatactgaatgtgttctttgtggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATGACATGGATACGTCCTCTGCAGACGCGGCTTACAACACGACCAACACATA
                || |  | ||        |       ||   |    | ||| ||||  |||  |      | |  || | |||  ||  | |||  ||| |      | ||||||| ||||||  |||||| ||||||||||| ||||| |||||  ||||||||||||| || || ||||| ||||| || |||||||| |||||| ||||
--------------ggaagatattagtccagtagtaacaacgcctgcaggaagaatg-tgca--ttattgctgcaattctgatgtgctc-cacgcattgttctctgtaaaatttccagTTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATGACATGGACACATCGTCTGCTGACGCCGCCTACAACACCACCAACCCATA
















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|116826923|gb|EC870765.1|EC870765
EST:     CTTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCA                         TTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
genomic: ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
EST: gi|60348538|gb|DN215511.1|DN215511
EST:     ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCA                         TTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
genomic: ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
EST: gi|161590551|gb|EY961433.1|EY961433
EST:     CGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCA                         TTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
genomic: CGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
EST: gi|6445448|gb|AW179366.1|AW179366
EST:     ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCA                         TTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
genomic: ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
EST: gi|20513026|gb|BQ280212.1|BQ280212
EST:     ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCA                         TTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
genomic: ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
EST: gi|78544301|gb|DV621799.1|DV621799
EST:     ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCA                         TTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
genomic: ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
EST: gi|88748313|gb|DY532454.1|DY532454
EST:     ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCA                         TTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
genomic: ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
EST: gi|113804186|gb|DW920377.1|DW920377
EST:     CTGATTCGTTAGAAGATGACAGCCAACTAACCA                         TTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGNGGAACTTGGTCTGAATG
genomic: CTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
EST: gi|29945539|gb|CB815690.1|CB815690
EST:     ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCA                         TTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
genomic: ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
EST: gi|211282779|gb|FL192970.1|FL192970
EST:     ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCA                         TTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
genomic: ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
EST: gi|31611961|gb|CD568583.1|CD568583
EST:     ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCA                         TTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
genomic: ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
EST: gi|37401209|gb|CF637968.1|CF637968
EST:     ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACATCCAACTAACCA                         TTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
genomic: ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
EST: gi|67020485|gb|CO449234.1|CO449234
EST:     TTTGTGGCCCCGGCTACTGATTCGTTNA-AAGATGACAGCCAACTAACCA                         TTTGA-GAGT-TCANAGGAGTTGGGAGCANAACGAGGGAACTTG-TCTGAA
genomic: TTTGTGGCCCCGGCTACTGATTCGTT-AGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTT-GAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGG-AACTTGGTCTGAA
EST: gi|60353658|gb|DN220631.1|DN220631
EST:     ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCA                         TTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
genomic: ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
EST: gi|60395671|gb|DN228541.1|DN228541
EST:     ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCA                         TTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
genomic: ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
EST: gi|113823141|gb|DW940321.1|DW940321
EST:     TTGTGTCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCA                         TTGAAGAGTATCAGAGGAGTTAGGGAGCAGAACGAGGAACTTGGTCTGAAT
genomic: TTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTT-GGGAGCAGAACGAGGAACTTGGTCTGAAT
EST: gi|37401269|gb|CF637997.1|CF637997
EST:     ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCA                         TTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
genomic: ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
EST: gi|149027381|gb|EE046513.2|EE046513
EST:     ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCA                         TTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
genomic: ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
EST: gi|78543967|gb|DV621465.1|DV621465
EST:     ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCA                         TTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
genomic: ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
EST: gi|60350354|gb|DN217327.1|DN217327
EST:     ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCA                         TTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
genomic: ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
EST: gi|88755471|gb|DY539612.1|DY539612
EST:     ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCA                         TTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
genomic: ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
EST: gi|28568977|gb|CB280852.1|CB280852
EST:     ATTTGTGGCCCCGGCTACTGATTCGCTAGAAGATGACAGCCAACTAACCA                         TTGAAGAGTATCAGAGGAGTT
genomic: ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTT
EST: gi|113807835|gb|DW927987.1|DW927987
EST:     CGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCA                         TTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
genomic: CGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
EST: gi|7135394|gb|AW498064.1|AW498064
EST:     ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCA                         TTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
genomic: ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
EST: gi|7135020|gb|AW497876.1|AW497876
EST:     ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCA                         TTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
genomic: ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
EST: gi|60357973|gb|DN224946.1|DN224946
EST:     ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCA                         TTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
genomic: ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
EST: gi|211282781|gb|FL192972.1|FL192972
EST:     ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCA                         TTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG
genomic: ATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATG

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: 209

AGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCGGCTTCATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATGACATGGATACGTCCTCTGCAGACGCGGCTTACAACACGACCAACACATA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 47

AGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCGGCTTCATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATGACATGGATACGTCCTCTGCAGACGCGGCTTACAACACGACCAACACATA


Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 17

AGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCGGCTTCATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATGACATGGATACGTCCTCTGCAGACGCGGCTTACAACACGACCAACACATA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 57

AGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCGGCTTCATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaac ... tggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATGACATGGATACGTCCTCTGCAGACGCGGCTTACAACACGACCAACACATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaaaggatgcgtgcatatatactcatactgaatgtgttctttgtggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATGACATGGATACGTCCTCTGCAGACGCGGCTTACAACACGACCAACACATA
                                      ttctttgt  CT-rich tract
                atatatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttaacctcatcaacaattcagatacacgatggtgctcccctgataccggatgctgcaagttaaaggatgcgtgcatatatactcatactgaatgtgttctttgtggagtgcagTTGAAGAGTATCAGAGGAGTTGGGAGCAGAACGAGGAACTTGGTCTGAATGACATGGATACGTCCTCTGCAGACGCGGCTTACAACACGACCAACACATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG