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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgttcagttgtgcattcatttgaacaggttccatatagttgaaaaactgtatatgccgccaggaattatgactgcatttctaatacttgccttcacagGTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGATGTGTCGATG

Basic information

species Zea mays
transcript GRMZM2G155384_T01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155384_T02 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os02g05340.1 (Oryza sativa), 3'ss of exon 19
gttgttcagttgtgcattcatttgaacaggttccatatagttgaaaaactgtatatgccgc---caggaattatgactgcatttctaatact----tgccttcacagGTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGATGTGTCGATG
  || ||  || | |||  |||||     ||| ||||   | | ||| |  | |||||| |   |||   |  ||  |  | ||  ||| ||    | || || |||||||| ||||||||||| || |||||| ||||||||||||| || || |||||||| |||
--tggtccattctacatctatttg-----gttgcataatttagcaaagcaatttatgccccactcagtgttgttgtatctacttacaattctattatcccatcccagGTAAATGTTATGGACACGCTTAGCAGACTGAGTCATGATGCGGATGCTGATGTGTCAATG
















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|32929670|gb|CF034482.1|CF034482
EST:     GACGGGCAGGTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAG                         GTAAACGGTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
genomic: GACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAGgtaactggat ... gccttcacagGTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
EST: gi|18384394|gb|BM417593.1|BM417593
EST:     GACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAG                         GTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
genomic: GACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAGgtaactggat ... gccttcacagGTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
EST: gi|32926108|gb|CF030920.1|CF030920
EST:     GACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAG                         GTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
genomic: GACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAGgtaactggat ... gccttcacagGTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
EST: gi|32841969|gb|CD981650.1|CD981650
EST:     GACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAG                         GTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
genomic: GACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAGgtaactggat ... gccttcacagGTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
EST: gi|211100368|gb|FL070846.1|FL070846
EST:     CTGCATATCTAATCCCAAG                         GTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
genomic: CTGCATATCTAATCCCAAGgtaactggat ... gccttcacagGTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
EST: gi|32926755|gb|CF031567.1|CF031567
EST:     GACGGGCAGGTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAG                         GTAAACGGTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
genomic: GACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAGgtaactggat ... gccttcacagGTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
EST: gi|211100372|gb|FL070850.1|FL070850
EST:     CTAATCCCAAG                         GTAAACGTTATGGACACACTGAGCAGATTGAGTCATGATGCAGACGCCGAT
genomic: CTAATCCCAAGgtaactggat ... gccttcacagGTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
EST: gi|32925375|gb|CF030187.1|CF030187
EST:     GACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAG                         GTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
genomic: GACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAGgtaactggat ... gccttcacagGTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
EST: gi|32925086|gb|CF029898.1|CF029898
EST:     GACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAG                         GTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
genomic: GACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAGgtaactggat ... gccttcacagGTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
EST: gi|32925553|gb|CF030365.1|CF030365
EST:     GACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAG                         GTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
genomic: GACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAGgtaactggat ... gccttcacagGTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
EST: gi|32926620|gb|CF031432.1|CF031432
EST:     GACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAG                         GTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
genomic: GACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAGgtaactggat ... gccttcacagGTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
EST: gi|18659836|gb|BM500547.1|BM500547
EST:     GACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAG                         GTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCA
genomic: GACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAGgtaactggat ... gccttcacagGTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCA
EST: gi|32849654|gb|CD989335.1|CD989335
EST:     CATATCTAATCCCAAG                         GTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
genomic: CATATCTAATCCCAAGgtaactggat ... gccttcacagGTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
EST: gi|32908274|gb|CF013087.1|CF013087
EST:     GACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAG                         GTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
genomic: GACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAGgtaactggat ... gccttcacagGTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
EST: gi|32928954|gb|CF033766.1|CF033766
EST:     GACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAG                         GTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGGCGCCGAT
genomic: GACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAGgtaactggat ... gccttcacagGTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
EST: gi|32925292|gb|CF030104.1|CF030104
EST:     GACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCGAG                         GTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
genomic: GACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAGgtaactggat ... gccttcacagGTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
EST: gi|32928817|gb|CF033629.1|CF033629
EST:     GACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAG                         GTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCGGACGCCGAT
genomic: GACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAGgtaactggat ... gccttcacagGTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
EST: gi|32925632|gb|CF030444.1|CF030444
EST:     GACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAG                         GTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT
genomic: GACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAGgtaactggat ... gccttcacagGTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGAT

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), 43 (downstream exon)
Score: 1353

GGCTGTACGTTCACTTGAGCGTCTTCTGCAGTATGGCGAGCAGAATATAAGACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAGgtaactggat ... gccttcacagGTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGATGTGTCGATG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 920

GGCTGTACGTTCACTTGAGCGTCTTCTGCAGTATGGCGAGCAGAATATAAGACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAGgtaactggat ... gccttcacagGTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGATGTGTCGATG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 486

GGCTGTACGTTCACTTGAGCGTCTTCTGCAGTATGGCGAGCAGAATATAAGACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAGgtaactggat ... gccttcacagGTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGATGTGTCGATG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 1037

GGCTGTACGTTCACTTGAGCGTCTTCTGCAGTATGGCGAGCAGAATATAAGACGGGCAGTTCCTCTTGCTCTTGGTATACTCTGCATATCTAATCCCAAGgtaactggat ... gccttcacagGTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGATGTGTCGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaactgtatatgccgccaggaattatgactgcatttctaatacttgccttcacagGTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGATGTGTCGATG
                                  ttctaat  putative branch site (score: 1037)
                                          cttgccttc  CT-rich tract
                                atttctaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgttcagttgtgcattcatttgaacaggttccatatagttgaaaaactgtatatgccgccaggaattatgactgcatttctaatacttgccttcacagGTAAACGTTATGGACACACTAAGCAGATTGAGTCATGATGCAGACGCCGATGTGTCGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT