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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtagagtaatcaccataatgcagatttattcagcattttttatcaatccttatatgtggaaatctttatctagctcttctgtagctgacgtactgaatatttcaatgttggctttagGTTGGTACGGTTGTTGAGCCTGCATCTGAGTTCTACTCAAGTAGGCTGAAAAATAGGGAACGCAAGGCAACATTGGTGGACGAGCTGCTATCAGATCAAT

Basic information

species Zea mays
transcript GRMZM2G075223_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075223_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g49780.1 (Oryza sativa), 3'ss of exon 3
gtaagtagagtaatcaccataatgcagatttattcagcattttttatcaatccttatatgtggaaatctttatctagctcttctgtagctgacgtactgaatatttcaatgttggctttagGTTGGTACGGTTGTTGAGCCTGCATCTGAGTTCTACTCAAGTAGGCTGAAAAATAGGGAACGCAAGGCAACATTGGTGGACGAGCTGCTATCAGATCAAT
                   ||| | ||   || |  |||   ||| | |   | ||| |     |   | |  || |||| |    | || |  |  |||| |||||  |  ||| | ||||||||||| ||| ||||||||||||||||||||| |||||||||||||| ||| ||||| |||||  |||||||||| || |||||  |||| |||||| 
------------------gtaa-gtagtcatactgggcagcattttttaggtcatatgtc----agcttatggct-gctcataatcaacttatatgatgaaaatttctgtaatgg-tatagGTTGGTACAGTTATTGAGCCTGCATCTGAGTTCTTCTCAAGTAGGCTGACAAAGAGGGAGCGCAAAACAACATTGGTTGATGAGCTCTTATCTGATCAAC
















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|211526078|gb|FL234898.1|FL234898
EST:     CACTTCAAGCGGGGCAGGAAAGTCCAAGGCCCCTTCCCAAGTACTTCCAA                         GNTGGGTACGGTTGTTNGAGCCTGCATCTGAGTTCTACNTCA-GTAGGCTG
genomic: CACTTCAAGCGGG-CAGGAAAGTCCAAGGCCC-TTCCCAAGTACTTCCAAgtaagtagag ... ttggctttagGTTGG-TACGGTTGTT-GAGCCTGCATCTGAGTTCTAC-TCAAGTAGGCTG
EST: gi|211523079|gb|FL234892.1|FL234892
EST:     GGCACTTCAAGCGGGCAGGAAAGTCCAAGGCCCTTCCCAAGTACTTCCAA                         GTCGGTACGGTTGTTGAGCCTGCATCTGAGTTCTACTCAAGTAGGCTGAAA
genomic: GGCACTTCAAGCGGGCAGGAAAGTCCAAGGCCCTTCCCAAGTACTTCCAAgtaagtagag ... ttggctttagGTTGGTACGGTTGTTGAGCCTGCATCTGAGTTCTACTCAAGTAGGCTGAAA
EST: gi|211523080|gb|FL234893.1|FL234893
EST:     GGCACTTCAAGCGGGCAGGAAAGTCCAAGGCCCTTCCCAAGTACTTCCAA                         GTTGGTACGGTTGTTGAGCCTGCATCTGAGTTCTACTCAAGTAGGCTGAAA
genomic: GGCACTTCAAGCGGGCAGGAAAGTCCAAGGCCCTTCCCAAGTACTTCCAAgtaagtagag ... ttggctttagGTTGGTACGGTTGTTGAGCCTGCATCTGAGTTCTACTCAAGTAGGCTGAAA
EST: gi|28984907|gb|BQ539256.2|BQ539256
EST:     GGCACTTCAAGCGGGCAGGAAAGTCCAAGGCCCTTCCCAAGTACTTCCAA                         GTTGGTACGGTTGTTGAGCCTGCATCTGAGTTCTACTCAAGTAGGCTGAAA
genomic: GGCACTTCAAGCGGGCAGGAAAGTCCAAGGCCCTTCCCAAGTACTTCCAAgtaagtagag ... ttggctttagGTTGGTACGGTTGTTGAGCCTGCATCTGAGTTCTACTCAAGTAGGCTGAAA
EST: gi|88755678|gb|DY539819.1|DY539819
EST:     GGCACTTCAAGCGGGCAGGAAAGTCCAAGGCCCTTCCCAAGTACTTCCCA                         GTTGGTACGGTTGTTGAGCCTGCCTCTGAGTTCTACTCAAGTAGGCTGAAA
genomic: GGCACTTCAAGCGGGCAGGAAAGTCCAAGGCCCTTCCCAAGTACTTCCAAgtaagtagag ... ttggctttagGTTGGTACGGTTGTTGAGCCTGCATCTGAGTTCTACTCAAGTAGGCTGAAA
EST: gi|71319546|gb|DR796519.1|DR796519
EST:     GGCACTTCAAGCGGGCAGGAAAGTCCAAGGCCCTTCCCAAGTACTTCCAA                         GTTGGTACGGTTGTTGAGCCTGCATCTGAGTTCTACTCAAGTAGGCTGAAA
genomic: GGCACTTCAAGCGGGCAGGAAAGTCCAAGGCCCTTCCCAAGTACTTCCAAgtaagtagag ... ttggctttagGTTGGTACGGTTGTTGAGCCTGCATCTGAGTTCTACTCAAGTAGGCTGAAA
EST: gi|28931156|gb|CB334517.1|CB334517
EST:     GGCCCTTCAAGCGGGCAGGAAAGTCCAAGGCCCTTCCCAAGTACTTCCAA                         GTTGGTACGGTTGTTGAGCCTGCATCTGAGTTCTACTCAAGTAGGCTGAAA
genomic: GGCACTTCAAGCGGGCAGGAAAGTCCAAGGCCCTTCCCAAGTACTTCCAAgtaagtagag ... ttggctttagGTTGGTACGGTTGTTGAGCCTGCATCTGAGTTCTACTCAAGTAGGCTGAAA
EST: gi|211188431|gb|FL445800.1|FL445800
EST:     GGCACTTCAAGCGGGCAGGAAAGTCCAAGGCCCTTCCCAAGTACTTCCAA                         GTTGGTACGGTTGTTGAGCCTGCATCTGAGTTCTACTCAAGTAGGCTGAAA
genomic: GGCACTTCAAGCGGGCAGGAAAGTCCAAGGCCCTTCCCAAGTACTTCCAAgtaagtagag ... ttggctttagGTTGGTACGGTTGTTGAGCCTGCATCTGAGTTCTACTCAAGTAGGCTGAAA
EST: gi|60347175|gb|DN214148.1|DN214148
EST:     GGCACTTCAAGCGGGCAGGAAAGTCCAAGGCCCTTCCCAAGTACTTCCAA                         GTTGGTACGGTTGTTGAGCCTGCATCTGAGTTCTACTCAAGTAGGCTGAAA
genomic: GGCACTTCAAGCGGGCAGGAAAGTCCAAGGCCCTTCCCAAGTACTTCCAAgtaagtagag ... ttggctttagGTTGGTACGGTTGTTGAGCCTGCATCTGAGTTCTACTCAAGTAGGCTGAAA
EST: gi|28909576|gb|CB330996.1|CB330996
EST:     GGCACTTCAAGCGGGCAGGAAAGTCCAAGGCCCTTCCCAAGTACTTCCAA                         GTTGGTACGGTTGTTGAGCCTGCATCTGAGTTCTACTCAAGTAGGCTGAAA
genomic: GGCACTTCAAGCGGGCAGGAAAGTCCAAGGCCCTTCCCAAGTACTTCCAAgtaagtagag ... ttggctttagGTTGGTACGGTTGTTGAGCCTGCATCTGAGTTCTACTCAAGTAGGCTGAAA
EST: gi|193501873|gb|AM938006.1|AM938006
EST:     GGCACTTCAAGCGGGCAGGAAAGTCCAAGGCCCTTCCCAAGTACTTCCAA                         GTTGGTACGGGTTGTTGAGCCTGCATCTGAGTTCTACTCAAGTAGGGCTGA
genomic: GGCACTTCAAGCGGGCAGGAAAGTCCAAGGCCCTTCCCAAGTACTTCCAAgtaagtagag ... ttggctttagGTTGGTACGG-TTGTTGAGCCTGCATCTGAGTTCTACTCAAGTAGG-CTGA

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), 46 (downstream exon)
Score: 141

CTGAGGCATGTAATTGACCCAAAAAGGCACTTCAAGCGGGCAGGAAAGTCCAAGGCCCTTCCCAAGTACTTCCAAgtaagtagag ... ttggctttagGTTGGTACGGTTGTTGAGCCTGCATCTGAGTTCTACTCAAGTAGGCTGAAAAATAGGGAACGCAAGGCAACATTGGTGGACGAGCTGCTATCAGATCAAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 101

CTGAGGCATGTAATTGACCCAAAAAGGCACTTCAAGCGGGCAGGAAAGTCCAAGGCCCTTCCCAAGTACTTCCAAgtaagtagag ... ttggctttagGTTGGTACGGTTGTTGAGCCTGCATCTGAGTTCTACTCAAGTAGGCTGAAAAATAGGGAACGCAAGGCAACATTGGTGGACGAGCTGCTATCAGATCAAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 125

CTGAGGCATGTAATTGACCCAAAAAGGCACTTCAAGCGGGCAGGAAAGTCCAAGGCCCTTCCCAAGTACTTCCAAgtaagtagag ... ttggctttagGTTGGTACGGTTGTTGAGCCTGCATCTGAGTTCTACTCAAGTAGGCTGAAAAATAGGGAACGCAAGGCAACATTGGTGGACGAGCTGCTATCAGATCAAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 87

CTGAGGCATGTAATTGACCCAAAAAGGCACTTCAAGCGGGCAGGAAAGTCCAAGGCCCTTCCCAAGTACTTCCAAgtaagtagag ... ttggctttagGTTGGTACGGTTGTTGAGCCTGCATCTGAGTTCTACTCAAGTAGGCTGAAAAATAGGGAACGCAAGGCAACATTGGTGGACGAGCTGCTATCAGATCAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttatctagctcttctgtagctgacgtactgaatatttcaatgttggctttagGTTGGTACGGTTGTTGAGCCTGCATCTGAGTTCTACTCAAGTAGGCTGAAAAATAGGGAACGCAAGGCAACATTGGTGGACGAGCTGCTATCAGATCAAT
                    agctgac  putative branch site (score: 87)
                                 aatatttcaatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtagagtaatcaccataatgcagatttattcagcattttttatcaatccttatatgtggaaatctttatctagctcttctgtagctgacgtactgaatatttcaatgttggctttagGTTGGTACGGTTGTTGAGCCTGCATCTGAGTTCTACTCAAGTAGGCTGAAAAATAGGGAACGCAAGGCAACATTGGTGGACGAGCTGCTATCAGATCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA