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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggcaactgacttttatccagtgtctacctgttaagtcatttgccattttcgtgcattttcaaaaatggttgtcatgaaaatgttactttaccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGACGTGGTGCTGCCCAAAACATAATTCCCAGCTCCACTGGTGCAGCAAAG

Basic information

species Zea mays
transcript GRMZM2G104632_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104632_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 9
------gttggcaactgacttttatccagtgtctacc-tgttaa--gtca--tttgccattttcgtgcattttcaaaaatggttgtcatgaaaatgttactttaccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGACGTGGTGCTGCCCAAAACATAATTCCCAGCTCCACTGGTGCAGCAAAG
       ||  |   ||| |||| || | |||| |   ||   |  | ||  ||| |  | | |    ||  |         | ||||| | |   || |||| | || | |||| ||||||||||| |||||||| ||||| ||||| |||||||||||||| ||||||||||| |||||||||||||| ||||||||||||||||| |||
gttttctttcccttatgaattttgtc-attgtcaaggatggagactgccaatttttcagtctcctcatatcatgttgttcattagtcataacagacttgctttcctatattcagCCACCCAGAAGACTGTCGATGGCCCTTCAATGAAAGATTGGAGAGGAGGGCGTGGTGCTGCTCAAAACATAATTCCTAGCTCCACTGGTGCAGCCAAG

upper sequence: GRMZM2G104632_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 9
------------gttggcaactg--acttttatccagtgtctacctgttaagtca--tttgccattttcgtgcattttcaaaaatggttgtcatgaaaatgttactttaccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGACGTGGTGCTGCCCAAAACATAATTCCCAGCTCCACTGGTGCAGCAAAG
             |||  || ||   | | ||       | |||   |   ||||      || |||  ||     ||     || | |  |||  |||| ||  |||  |     |||| || || |||||||| ||||||||||| |||||||||||| |||||||| | || || || ||||| |||||||| || || |||||||| || |||
gtctcttccaaaattgctaattgtagcctctagttt-catttactcatgcggtcaaaccatccctttatgtttcacttgtggcattggtaacatccaaatctttttttttc----tcagCAACACAAAAGACCGTAGATGGTCCTTCTATGAAGGATTGGCGAGGAGGAAGAGGGGCAGCTCAAAATATAATTCCAAGTTCAACTGGTGCTGCGAAG

upper sequence: GRMZM2G104632_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA16G09020.1 (Glycine max), 3'ss of exon 9
--------------gttggcaactg-acttttatccagtgtctacctgttaagtcatttgccattttcgtgcattttcaaaaatggttgtcatgaaa---atgttactttaccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGACGTGGTGCTGCCCAAAACATAATTCCCAGCTCCACTGGTGCAGCAAAG
               |||  || || | | |         | |||   |   ||||    ||||     |   ||| || |  |||   |  | | |   |  |   |||    |   |||| || || ||||| || ||||||||||| |||||||||||| |||||||| | || || || ||||| |||||||| || || |||||||| || |||
gtctcttttccaaatttgctaattgtagtctctagtttcatttactcatgcggtca--aaccatccctttatgttt-cacatgtggcattggtaacatccaattctttttttttttctcagCAACACAAAAGACTGTAGATGGTCCTTCTATGAAGGATTGGCGAGGAGGAAGAGGGGCAGCTCAAAATATAATTCCAAGTTCAACTGGTGCTGCGAAG

upper sequence: GRMZM2G104632_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv19s0085g00600.t01 (Vitis vinifera), 3'ss of exon 9
gttggcaactgacttttatccagtgtctacctgttaagtcatttgccattttcgtgcattttcaaaaatggttgtcatgaaaatgttactttaccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGACGTGGTGCTGCCCAAAACATAATTCCCAGCTCCACTGGTGCAGCAAAG
          |  | |  | |    ||||  ||  | ||    || ||  | | |   | ||   || |   |  ||||   ||| | ||||   |||| |||| || ||||||||||| ||||| ||||| |||||||||||| |||| || || |||||| | ||||| || || || |||||||||||||| ||||||
----------gtttctccttctccctctatttgacatgt-gcctgacacatgcttttgtatt---aatttagtaacatggttatgct-ctttttgatgttcagCCACACAGAAGACCGTGGATGGGCCTTCAATGAAGGATTGGCGAGGGGGCCGAGGTGCTTCACAAAATATCATCCCAAGCTCCACTGGTGCTGCAAAG

upper sequence: GRMZM2G104632_T01 (Zea mays), 3'ss of exon 9
lower sequence: PP1S309_73V6.3 (Physcomitrella patens), 3'ss of exon 6
gttggcaactgacttttatccagtgtcta--cctgttaag---tcatttgccatt-ttcgtgcattttcaaaaa--tggttgtcatgaaaatgttact--ttaccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGACGTGGTGCTGCCCAAAACATAATTCCCAGCTCCACTGGTGCAGCAAAG
  |    |  |    ||     || | |   | ||||  |   |||||||    |  |  | ||||    || |  |  ||   ||||  |||| | |  || |  ||| ||||||||||||||||||| || ||||| ||    ||||| ||| | ||||||||||||||||  || ||||| ||||||||||| ||||| || || |||
-gtaatgatggttcctttagaggtctttgagcatgtttgggtgtcatttgtgggtgcttttacattgagcaagacttaatttggatgatgatgtaaatggtttctgtgtgcagCTACCCAGAAGACCGTGGACGGTCCATCTGGAAAGGACTGGCGTGGAGGACGTGGTGCTGGACAGAACATTATTCCCAGCTCAACTGGAGCTGCGAAG

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|211318612|gb|FL124689.1|FL124689
EST:     AACTGTTCATGCAACAACAG                         CTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
genomic: AACTGTTCATGCAACAACAGgttggcaact ... ccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
EST: gi|29576993|gb|CB617105.1|CB617105
EST:     GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG                         CTACCCAGAAG
genomic: GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAGgttggcaact ... ccatgtccagCTACCCAGAAG
EST: gi|31354565|gb|CD438922.1|CD438922
EST:     GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG                         CTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
genomic: GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAGgttggcaact ... ccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
EST: gi|60397796|gb|DN230612.1|DN230612
EST:     GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG                         CTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
genomic: GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAGgttggcaact ... ccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
EST: gi|67023119|gb|CO451868.1|CO451868
EST:     TGACAATTGTTCATGCAACAACAG                         CTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
genomic: TGACAACTGTTCATGCAACAACAGgttggcaact ... ccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
EST: gi|211318619|gb|FL124696.1|FL124696
EST:     GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG                         CTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
genomic: GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAGgttggcaact ... ccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
EST: gi|31352951|gb|CD437308.1|CD437308
EST:     GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG                         CTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
genomic: GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAGgttggcaact ... ccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
EST: gi|211011830|gb|FL066256.1|FL066256
EST:     GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG                         CTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
genomic: GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAGgttggcaact ... ccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
EST: gi|67017162|gb|CO445911.1|CO445911
EST:     GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG                         CTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
genomic: GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAGgttggcaact ... ccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
EST: gi|71449916|gb|DR830966.1|DR830966
EST:     TCATGCAACAACAG                         CTACCCAGAAGACCGTCGATGGTCTTTCGATGAAGGATTGGAGAGGAGGAC
genomic: TCATGCAACAACAGgttggcaact ... ccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
EST: gi|211009063|gb|FL066254.1|FL066254
EST:     GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG                         CTACCCAGAAGACCGTCGATGGTCCTTCCATGAAGGATTGGAGAGGAGGAC
genomic: GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAGgttggcaact ... ccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
EST: gi|78543682|gb|DV621180.1|DV621180
EST:     TCATGCAACAACAG                         CTACCCAGAAGACCGTCGATGTTCTTTCGATGAAGGATTGGAGAGGAGGAC
genomic: TCATGCAACAACAGgttggcaact ... ccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
EST: gi|21088933|gb|BQ401246.1|BQ401246
EST:     GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG                         CTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
genomic: GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAGgttggcaact ... ccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
EST: gi|6564069|gb|AW231691.1|AW231691
EST:     GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG                         CTACCCAGAAGACCGTCGATGGTCCTTC
genomic: GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAGgttggcaact ... ccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTC
EST: gi|6526690|gb|AW215981.1|AW215981
EST:     GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG                         CTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
genomic: GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAGgttggcaact ... ccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
EST: gi|24769367|gb|CA404496.1|CA404496
EST:     GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG                         CTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
genomic: GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAGgttggcaact ... ccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
EST: gi|32945687|gb|CF050506.1|CF050506
EST:     GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG                         CTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
genomic: GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAGgttggcaact ... ccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
EST: gi|5928870|gb|AW056162.1|AW056162
EST:     GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG                         CTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
genomic: GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAGgttggcaact ... ccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
EST: gi|32857247|gb|CD996928.1|CD996928
EST:     GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG                         CTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
genomic: GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAGgttggcaact ... ccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
EST: gi|71449917|gb|DR830967.1|DR830967
EST:     GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG                         CTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
genomic: GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAGgttggcaact ... ccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
EST: gi|60355829|gb|DN222802.1|DN222802
EST:     GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG                         CTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
genomic: GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAGgttggcaact ... ccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
EST: gi|71320203|gb|DR796854.1|DR796854
EST:     GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG                         CTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
genomic: GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAGgttggcaact ... ccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
EST: gi|211011829|gb|FL066255.1|FL066255
EST:     GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG                         CTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGA
genomic: GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAGgttggcaact ... ccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGA
EST: gi|211318615|gb|FL124692.1|FL124692
EST:     GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG                         CTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC
genomic: GGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAGgttggcaact ... ccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGAC

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), 49 (downstream exon)
Score: 361

GTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAGgttggcaact ... ccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGACGTGGTGCTGCCCAAAACATAATTCCCAGCTCCACTGGTGCAGCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 200

GTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAGgttggcaact ... ccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGACGTGGTGCTGCCCAAAACATAATTCCCAGCTCCACTGGTGCAGCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 274

GTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAGgttggcaact ... ccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGACGTGGTGCTGCCCAAAACATAATTCCCAGCTCCACTGGTGCAGCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 415

GTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAGgttggcaact ... ccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGACGTGGTGCTGCCCAAAACATAATTCCCAGCTCCACTGGTGCAGCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcgtgcattttcaaaaatggttgtcatgaaaatgttactttaccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGACGTGGTGCTGCCCAAAACATAATTCCCAGCTCCACTGGTGCAGCAAAG
                                        ctttacc  CT-rich tract
                               aaaatgttacttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggcaactgacttttatccagtgtctacctgttaagtcatttgccattttcgtgcattttcaaaaatggttgtcatgaaaatgttactttaccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGACGTGGTGCTGCCCAAAACATAATTCCCAGCTCCACTGGTGCAGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG