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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcttagtaaccttgaaaatattagatgtcttctgaaaatacaatgcagttttagctaccttctttattattaattactacttgttttgctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCAAATGTTATTTTTTCCCGAGGGTAACAAATGTGGCCCCCAGTTTTACCCT

Basic information

species Zea mays
transcript GRMZM2G095348_T01
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 23
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 24
ttgcttagtaaccttgaaaatattagatgtcttctgaaaatacaatgcagttttagctaccttctttatt--attaa--ttactacttgttttgctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTG-GCTGCAAATGTTATTTTTTCCCGAGGGTAACA--AATGTGGCCCCCAGTTTTACCCT
 ||    || |   | | |    ||| |   || |        ||  |||||||   ||   |  |||||  | | |  ||| |  ||  ||| |||||||||||||||||||||||||| || || || |||         ||  |||   ||   ||| | |    |        | |    |   |  ||  ||  |  ||   
-tgtagggtcaagcttatagc--tagcttatttttttgttcttaaaccagttttt-ttattctaattattgaactgaatttattcttttcttttctccttgcagTGCTAACTGAACATGAGTAAGGACCAAGGATGCTGTGCCGTTTTGCATTGGTGATGCTGTGCCGTTTGAGCTTTGATCTTATCATATCCTTCAACTGAAC---
















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|32846872|gb|CD986553.1|CD986553
EST:     ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGG                         TGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
genomic: ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
EST: gi|32856876|gb|CD996557.1|CD996557
EST:     GGGAACGAGGGTGAGGAACAGCAGG                         TGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
genomic: GGGAACGAGGGTGAGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
EST: gi|32839442|gb|CD979123.1|CD979123
EST:     ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGG                         TGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
genomic: ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
EST: gi|60345624|gb|DN212597.1|DN212597
EST:     ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGG                         TGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
genomic: ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
EST: gi|32838986|gb|CD978667.1|CD978667
EST:     ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGG                         TGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
genomic: ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
EST: gi|113841925|gb|DW968155.1|DW968155
EST:     AGGAACAGCAGG                         TGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
genomic: AGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
EST: gi|18963727|gb|BM660597.1|BM660597
EST:     ACATGAAGAGACAGTTTCAGTAAATGGGAACGACAGTGAGGAACAGCAGG                         TGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
genomic: ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
EST: gi|71443012|gb|DR824062.1|DR824062
EST:     ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGG                         TGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
genomic: ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
EST: gi|67013339|gb|CO442088.1|CO442088
EST:     ACATGAAGAGACAGTTTCAGTAAATGGGAACGANGGTGAGGAACAGCANG                         TGCTAACTGAACATGAATANGGGCCGNAGG-AAGCACAACGCATTGGCTGC
genomic: ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCG-AGGGAAGCACAACGCATTGGCTGC
EST: gi|67016677|gb|CO445426.1|CO445426
EST:     ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGG                         TGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
genomic: ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
EST: gi|6563651|gb|AW231378.1|AW231378
EST:     ACATGAAGAGACAGTTTCAGTAAATGGGAAGGAGGGTGAGGAACAGCAGG                         TGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
genomic: ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
EST: gi|6681776|gb|AW287763.1|AW287763
EST:     ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGG                         TGCTAACTGAACATGAATAGGGGCCGAGGGAAGCNCAACGCATTGGCTGCA
genomic: ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
EST: gi|211347064|gb|FK984260.1|FK984260
EST:     ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGG                         TGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
genomic: ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
EST: gi|38502567|gb|CF972427.1|CF972427
EST:     GGAACGAGGGTGAGGAACAGCAGG                         TGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
genomic: GGAACGAGGGTGAGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
EST: gi|60347180|gb|DN214153.1|DN214153
EST:     ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGG                         TGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
genomic: ACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
EST: gi|32934584|gb|CF039396.1|CF039396
EST:     AGGAACAGCAGG                         TGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA
genomic: AGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCA

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: 21 (upstream exon), 47 (downstream exon)
Score: 139

GCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCAAATGTTATTTTTTCCCGAGGGTAACAAATGTGGCCCCCAGTTTTACCCT


Block sizes: 21 (upstream exon), 42 (downstream exon)
Score: 71

GCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCAAATGTTATTTTTTCCCGAGGGTAACAAATGTGGCCCCCAGTTTTACCCT


Block sizes: 21 (upstream exon), 26 (downstream exon)
Score: 35

GCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCAAATGTTATTTTTTCCCGAGGGTAACAAATGTGGCCCCCAGTTTTACCCT


Block sizes: 21 (upstream exon), 37 (downstream exon)
Score: 119

GCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGGgtacggacaa ... ctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCAAATGTTATTTTTTCCCGAGGGTAACAAATGTGGCCCCCAGTTTTACCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcagttttagctaccttctttattattaattactacttgttttgctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCAAATGTTATTTTTTCCCGAGGGTAACAAATGTGGCCCCCAGTTTTACCCT
                        tattaat  putative branch site (score: 119)
                                    cttgttttgctcctt  putative PPT
                ttctttattattaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgcttagtaaccttgaaaatattagatgtcttctgaaaatacaatgcagttttagctaccttctttattattaattactacttgttttgctccttgcagTGCTAACTGAACATGAATAGGGGCCGAGGGAAGCACAACGCATTGGCTGCAAATGTTATTTTTTCCCGAGGGTAACAAATGTGGCCCCCAGTTTTACCCT

- - - - - - - - - - - - - - -tcttctg
- - - - - - - - - - - - - - - - - - - - - caatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg