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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attcatgtttttttagcatgagcatgagatgcttcccagattattatatccaagcaatccaattctgatggatcttctgaaaatggatcgaacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATGTGGATGGAAGACTGCGAGAAGCAAGGATGAACCATCCTAAAGGGTTCAC

Basic information

species Zea mays
transcript GRMZM2G020943_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020943_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g15820.1 (Oryza sativa), 3'ss of exon 3
-attcatgtttttttagcatgagcatgagatgcttcccagattattatatccaag-caatccaattctgatggatcttctgaaaa-tggatcgaacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATGTGGATGGAAGACTGCGAGAAGCAAGGATGAACCATCCTAAAGGGTTCAC
  |  | |     |  |  |   |||    | |||  || |||     ||   ||   | |  ||||||||| ||||| | |||| |||||| |||| | ||||||||||||| |||||  |||||||||| ||  |||| ||||| |||||||| || || || ||||| || || | |||||||||||| || || || ||
actgtacgaaaaatcggtgtcgacattt--tacttatca-attgacgcatttgagatcaccagattctgatgtatcttgtaaaaaatggatcaaacattacagATAGCAGACCGAAGCTTGTTGCTGGTTCGCCGGAAGGATTATCCGGCCATGTCGACGGGAGGCTGCGGGAGGCGAAGATGAACCATCCGAAGGGATTTAC

upper sequence: GRMZM2G020943_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv14s0066g01590.t01 (Vitis vinifera), 3'ss of exon 3
attcatgtttttttagcatgagcatgagatgcttcccagattattatatccaagcaatccaattctg-atggatcttctg--aaaatggatcgaacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATGTGGATGGAAGACTGCGAGAAGCAAGGATGAACCATCCTAAAGGGTTCAC
  |||  || | ||    |      |   | | |||    |   |   |        | || ||||  |||  |  | ||  ||| | |||     | ||||||||||||||| || ||  ||||||| || ||  | || |  ||||| ||||| ||||| |  ||  |||||||||||||||||||||| |||||| | ||
--tcagattatgttgttgtttatg-gttctacctccttagtagcttggttgttttggtacagttctacatgttttgtatgttaaagttgatgatgaactgcagATAGCAGACCCAAACTGGTTGCTGGCTCGCCTGATGGGTACTCTGGGCATGTAGATGGGAAGCTAAGAGAAGCAAGGATGAACCATCCAAAAGGGCTTAC
















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|149005168|gb|EE039704.2|EE039704
EST:     CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCAT                         ATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
genomic: CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCATgtgagcacgc ... aacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
EST: gi|211160636|gb|FL114499.1|FL114499
EST:     CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCAT                         ATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGGCATG
genomic: CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCATgtgagcacgc ... aacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
EST: gi|78114597|gb|DV532985.1|DV532985
EST:     CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCAT                         ATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
genomic: CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCATgtgagcacgc ... aacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
EST: gi|76912974|gb|DV164954.1|DV164954
EST:     CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCAT                         ATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
genomic: CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCATgtgagcacgc ... aacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
EST: gi|211159050|gb|FL114492.1|FL114492
EST:     CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCAT                         ATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
genomic: CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCATgtgagcacgc ... aacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
EST: gi|31360064|gb|CD444421.1|CD444421
EST:     CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCAT                         ATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
genomic: CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCATgtgagcacgc ... aacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
EST: gi|71764659|gb|DR962596.1|DR962596
EST:     CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCAT                         ATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
genomic: CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCATgtgagcacgc ... aacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
EST: gi|211160639|gb|FL114502.1|FL114502
EST:     CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCAT                         ATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGNCATG
genomic: CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCATgtgagcacgc ... aacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
EST: gi|149099000|gb|EE185013.2|EE185013
EST:     CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCAT                         ATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
genomic: CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCATgtgagcacgc ... aacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
EST: gi|148958537|gb|EC904780.2|EC904780
EST:     CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCAT                         ATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
genomic: CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCATgtgagcacgc ... aacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
EST: gi|211160642|gb|FL114505.1|FL114505
EST:     CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCAT                         ATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
genomic: CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCATgtgagcacgc ... aacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
EST: gi|6021074|gb|AW066002.1|AW066002
EST:     CGACTCCATCAACAGCAACATCTACAGGGTACAGGTGCCGTTGTCACCAT                         ATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
genomic: CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCATgtgagcacgc ... aacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
EST: gi|32940716|gb|CF045535.1|CF045535
EST:     ACAGCTGCCGTTGTCACCAT                         ATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
genomic: ACAGCTGCCGTTGTCACCATgtgagcacgc ... aacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
EST: gi|78118043|gb|DV536430.1|DV536430
EST:     CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCAT                         ATAGCAGACCAAAGCTCCT
genomic: CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCATgtgagcacgc ... aacaatgcagATAGCAGACCAAAGCTCCT
EST: gi|89759931|gb|DY688587.1|DY688587
EST:     CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCAT                         ATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
genomic: CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCATgtgagcacgc ... aacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
EST: gi|211160643|gb|FL114506.1|FL114506
EST:     GACTCCATCAACAGCAACATCTACAGGGTACNAGCTGCCGTTGTCACCAT                         ATAGCAGACCAAAGCNTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCAT
genomic: GACTCCATCAACAGCAACATCTACAGGGTAC-AGCTGCCGTTGTCACCATgtgagcacgc ... aacaatgcagATAGCAGACCAAAGC-TCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCAT
EST: gi|74241599|gb|DT649513.1|DT649513
EST:     CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCAT                         ATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
genomic: CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCATgtgagcacgc ... aacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
EST: gi|149076865|gb|EE165521.2|EE165521
EST:     CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCAT                         ATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
genomic: CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCATgtgagcacgc ... aacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
EST: gi|211160633|gb|FL114496.1|FL114496
EST:     CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCAT                         ATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
genomic: CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCATgtgagcacgc ... aacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
EST: gi|211160644|gb|FL114507.1|FL114507
EST:     CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCAT                         ATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
genomic: CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCATgtgagcacgc ... aacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
EST: gi|71325268|gb|DR799321.1|DR799321
EST:     CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCAT                         ATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
genomic: CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCATgtgagcacgc ... aacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
EST: gi|211162233|gb|FL114511.1|FL114511
EST:     CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCAT                         ATAGCAGACCAAAGCTCCTTGCTGGTTCTNCAAAAGGTTTATCTGGCCATG
genomic: CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCATgtgagcacgc ... aacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
EST: gi|211160638|gb|FL114501.1|FL114501
EST:     CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCAT                         ATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG
genomic: CGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCATgtgagcacgc ... aacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATG

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 3 RNA-Seq libraries.


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 30

ATCGAGCCGCACGCCGTCGAGATCACCCCCGCCGGCAACCTCCTCGTGCTCGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCATgtgagcacgc ... aacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATGTGGATGGAAGACTGCGAGAAGCAAGGATGAACCATCCTAAAGGGTTCAC


Block sizes: 38 (upstream exon), 47 (downstream exon)
Score: 5

ATCGAGCCGCACGCCGTCGAGATCACCCCCGCCGGCAACCTCCTCGTGCTCGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCATgtgagcacgc ... aacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATGTGGATGGAAGACTGCGAGAAGCAAGGATGAACCATCCTAAAGGGTTCAC


Block sizes: 29 (upstream exon), 47 (downstream exon)
Score: 6

ATCGAGCCGCACGCCGTCGAGATCACCCCCGCCGGCAACCTCCTCGTGCTCGACTCCATCAACAGCAACATCTACAGGGTACAGCTGCCGTTGTCACCATgtgagcacgc ... aacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATGTGGATGGAAGACTGCGAGAAGCAAGGATGAACCATCCTAAAGGGTTCAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatccaagcaatccaattctgatggatcttctgaaaatggatcgaacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATGTGGATGGAAGACTGCGAGAAGCAAGGATGAACCATCCTAAAGGGTTCAC
                 ttctgat  putative branch site (score: 6)
                                tgaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attcatgtttttttagcatgagcatgagatgcttcccagattattatatccaagcaatccaattctgatggatcttctgaaaatggatcgaacaatgcagATAGCAGACCAAAGCTCCTTGCTGGTTCTCCAAAAGGTTTATCTGGCCATGTGGATGGAAGACTGCGAGAAGCAAGGATGAACCATCCTAAAGGGTTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
attcatg
- - - - - - - - - -gagcatg
- - - - - - - - - - - - - - -tgcttcc
- - - - - - - - - - - - - - - - - - - - - - - - - caagcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatgg