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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagtttcacatcattgtgttctgtcggtcttcttgagttttccgcataacttgttgggagtatatactaagccttatcccttcctttattcgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTCGCTGCTCCCACAAAAGATTCAGGCTTTTGAG

Basic information

species Zea mays
transcript GRMZM2G003565_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003565_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g35570.3 (Oryza sativa), 3'ss of exon 2
-------------aagtttcacatcattgtgttctgtcggtcttcttgagttttccgcataacttgttgggagtatatactaagccttatcccttcctttattcgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTCGCTGCTCCCACAAAAGATTCAGGCTTTTGAG
             || | | |||| ||| |||| ||| |   ||  ||||||||  |  | |||  |     || |  ||| |      ||   || |   ||  | |  ||||||||| || ||||||||||||||||| || ||||||||||||||||||||  |||||||||||||||||||  ||||||||
ttgaatagtggcaaattcttacattattctgttgtgttgcgatttctgagtttt--gggtgactgct-----gtttgcactga------tcttctcatgactttttgttttagTTGGGGGCGCAACCAAAACGGACAGCTTGGTCTTGGAACCACTGAAGACTCATTGCTCCCACAAAAGATTCAATCTTTTGAG
















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|211087165|gb|FL255708.1|FL255708
EST:     TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAG                         TGGGGGCCGTAACCAAAACGGACAGCTAGGCCCTTGGAACCCACTGA-GAC
genomic: TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCC-TTGGAACC-ACTGAAGAC
EST: gi|211087164|gb|FL255707.1|FL255707
EST:     TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAG                         TTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTC
genomic: TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTC
EST: gi|211087173|gb|FL255716.1|FL255716
EST:     TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAG                         TTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGA
genomic: TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGA
EST: gi|211476171|gb|FL255691.1|FL255691
EST:     TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAG                         TTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAAC-ACTGAAGACTC
genomic: TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTC
EST: gi|211473659|gb|FL255683.1|FL255683
EST:     TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAG                         TTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTC
genomic: TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTC
EST: gi|211089615|gb|FL255722.1|FL255722
EST:     TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGGCGGAGAAGTGCAGAG                         TTGGGGGCGTAAACCAAACCG-ACAGCTAGGC
genomic: TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAA-CCAAAACGGACAGCTAGGC
EST: gi|211087162|gb|FL255705.1|FL255705
EST:     TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAG                         TTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAAC
genomic: TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAAC
EST: gi|211471124|gb|FL255668.1|FL255668
EST:     TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAG                         TTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACT
genomic: TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACT
EST: gi|211471130|gb|FL255674.1|FL255674
EST:     TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAG                         TTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTC
genomic: TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTC
EST: gi|211473652|gb|FL255676.1|FL255676
EST:     TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAG                         TTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTC
genomic: TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTC
EST: gi|76935832|gb|DV174484.1|DV174484
EST:     TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAG                         TTGGGGCCGTAACCAAAACGGACAGCTAGGCCTT
genomic: TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTT
EST: gi|211473655|gb|FL255679.1|FL255679
EST:     TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAG                         TTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTC
genomic: TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTC
EST: gi|211087168|gb|FL255711.1|FL255711
EST:     TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAG                         TTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTC
genomic: TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTC
EST: gi|211148346|gb|FL363505.1|FL363505
EST:     TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAG                         TTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTC
genomic: TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTC
EST: gi|211476175|gb|FL255695.1|FL255695
EST:     TGCGGGGACAGCCATTGTCTTGCCGTCACCATG-CCGGAGAAGTGCAGAG                         TTGGGGCCCGTA-CCAAAACGGACAGCTAGGCCTTGGGAAC-ACTGAAGAC
genomic: TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCC-GTAACCAAAACGGACAGCTAGGCCTTGG-AACCACTGAAGAC
EST: gi|211471117|gb|FL255661.1|FL255661
EST:     TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAG                         TTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTTGGA-CCACTGAA
genomic: TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTT-GGAACCACTGAA
EST: gi|50339533|gb|CO534659.1|CO534659
EST:     TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAG                         TTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTC
genomic: TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTC
EST: gi|211476169|gb|FL255689.1|FL255689
EST:     TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAG                         TTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTC
genomic: TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTC
EST: gi|211471128|gb|FL255672.1|FL255672
EST:     TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAG                         TTGGGGCCGTAACCAAAACGGACAGCTA
genomic: TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTA
EST: gi|211087171|gb|FL255714.1|FL255714
EST:     TGCGGGGACAGCCATTGTCTTGCCGTCAC-ATGGCCGGAGAAGTGCAGAG                         TTGGGGCCGTAAC-AAAACGGACAGCTAGGCCTTGGAACCACTG
genomic: TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTG
EST: gi|211473662|gb|FL255686.1|FL255686
EST:     TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAG                         TTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTG
genomic: TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTG
EST: gi|71446512|gb|DR827562.1|DR827562
EST:     TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAG                         TTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTC
genomic: TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTC
EST: gi|211473660|gb|FL255684.1|FL255684
EST:     TGCGGGGACAGCCATTGTCTTGCCGTCAC-ATGGCCGGAGAAGTGCAGAG                         TTGGGGGCGTAAC-AAAACGGACAGCTAGGCCTTGAAAC-ACTGGAGACTC
genomic: TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTC
EST: gi|211471122|gb|FL255666.1|FL255666
EST:     TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAG                         TTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTC
genomic: TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTC
EST: gi|211473663|gb|FL255687.1|FL255687
EST:     TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAG                         TTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTC
genomic: TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTC
EST: gi|211471123|gb|FL255667.1|FL255667
EST:     TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGC-GGAGAAGTGCAGAG                         TTGGGGCCGTAAACAAAACGGACAGCTAGGCCTTGGAAACACTGA
genomic: TGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGA

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), 48 (downstream exon)
Score: 217

CGCCCCAGCCTGTCAAGGCGCTGCAGGGGCTCAAGATCAAACAGATTGCCTGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTCGCTGCTCCCACAAAAGATTCAGGCTTTTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 152

CGCCCCAGCCTGTCAAGGCGCTGCAGGGGCTCAAGATCAAACAGATTGCCTGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTCGCTGCTCCCACAAAAGATTCAGGCTTTTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 104

CGCCCCAGCCTGTCAAGGCGCTGCAGGGGCTCAAGATCAAACAGATTGCCTGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTCGCTGCTCCCACAAAAGATTCAGGCTTTTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 249

CGCCCCAGCCTGTCAAGGCGCTGCAGGGGCTCAAGATCAAACAGATTGCCTGCGGGGACAGCCATTGTCTTGCCGTCACCATGGCCGGAGAAGTGCAGAGgtgagcatgt ... cgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTCGCTGCTCCCACAAAAGATTCAGGCTTTTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataacttgttgggagtatatactaagccttatcccttcctttattcgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTCGCTGCTCCCACAAAAGATTCAGGCTTTTGAG
 gcataac  putative branch site (score: 249)
                          ccttatcccttccttt  putative PPT
               tatatactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagtttcacatcattgtgttctgtcggtcttcttgagttttccgcataacttgttgggagtatatactaagccttatcccttcctttattcgtatcgtagTTGGGGCCGTAACCAAAACGGACAGCTAGGCCTTGGAACCACTGAAGACTCGCTGCTCCCACAAAAGATTCAGGCTTTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - tgttctg
- - - - - - - - - - - - - - cttcttg
- - - - - - - - - - - - - - - - - - - - - - - - - -tgttggg