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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctagagttcactccatttctttcttttaaatgggtcgctttgttttctttgagtcaacagtattgtgacatgtcgttccattatcagGAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGCTCTTGCTAGGCGCATTGCTAAAGTGGGAACCGCTTCTCGTCCTCTTCTG

Basic information

species Zea mays
transcript GRMZM2G161566_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G161566_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g51410.2 (Oryza sativa), 3'ss of exon 6
gtatctagagttcactcc-atttctttcttttaaatgggtcgctttgt-------tttctttgagtcaacagtattgtga-catgtcgttccattatcagGAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGCTCTTGCTAGGCGCATTGCTAAAGTGGGAACCGCTTCTCGTCCTCTTCTG
|||||| ||||||||| | |||| |    ||  ||| | |   |||||        || |||   | |||| |||||||| |   | |||  |||||||||||||| ||||||||||||||||| |||||||| |||||||||||||| |||||||||||||| |||||||||||||| || || || ||||||||||| 
gtatctggagttcacttctatttttcctgttggaatagtttattttgtggcttctcttattttgattaacaatattgtgatctctttgttgtattatcagGAAATACATGAAGAAGGGCCTATCTGTTTGGTTGGATGTGCCCTTGGACGCTCTTGCTAGGCGTATTGCTAAAGTGGGGACTGCCTCCCGTCCTCTTCTA
















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|5343250|gb|AI795555.1|AI795555
EST:     CGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTG                         GAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGC
genomic: CGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTGgtatctagag ... ccattatcagGAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGC
EST: gi|211205927|gb|FL457759.1|FL457759
EST:     CGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTG                         BAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGC
genomic: CGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTGgtatctagag ... ccattatcagGAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGC
EST: gi|24934599|gb|CA452817.1|CA452817
EST:     CGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTG                         GAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGC
genomic: CGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTGgtatctagag ... ccattatcagGAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGC
EST: gi|37392587|gb|CF633545.1|CF633545
EST:     CGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTG                         GAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGC
genomic: CGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTGgtatctagag ... ccattatcagGAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGC
EST: gi|30087805|gb|CB886011.1|CB886011
EST:     CGATTAGTTGTTGCCNCCGGAGGTGGTGCTGTCATCCGACCAGTTAACTG                         GAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGC
genomic: CGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTGgtatctagag ... ccattatcagGAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGC
EST: gi|32164833|gb|CD670151.1|CD670151
EST:     CGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTG                         GAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGC
genomic: CGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTGgtatctagag ... ccattatcagGAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGC
EST: gi|13237004|gb|BG355018.1|BG355018
EST:     CGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTTTCTG                         GAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGC
genomic: CGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTGgtatctagag ... ccattatcagGAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGC
EST: gi|60395600|gb|DN228470.1|DN228470
EST:     CGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTG                         GAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGC
genomic: CGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTGgtatctagag ... ccattatcagGAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGC
EST: gi|211307747|gb|FL198214.1|FL198214
EST:     CGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTG                         GAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGC
genomic: CGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTGgtatctagag ... ccattatcagGAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGC
EST: gi|37398941|gb|CF636791.1|CF636791
EST:     CGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTG                         GAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGC
genomic: CGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTGgtatctagag ... ccattatcagGAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGC
EST: gi|24934498|gb|CA452716.1|CA452716
EST:     CGATTAGTTGTTGCCACCGGAGGTGGTGCTGCCATCCGACCAGTTAACTG                         GAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGC
genomic: CGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTGgtatctagag ... ccattatcagGAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGC
EST: gi|32928190|gb|CF033002.1|CF033002
EST:     CGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTG                         GAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGC
genomic: CGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTGgtatctagag ... ccattatcagGAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGC
EST: gi|44900819|gb|CK827364.1|CK827364
EST:     CGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTG                         GAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGC
genomic: CGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTGgtatctagag ... ccattatcagGAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGC

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: 48 (upstream exon), 49 (downstream exon)
Score: 74

AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTGgtatctagag ... ccattatcagGAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGCTCTTGCTAGGCGCATTGCTAAAGTGGGAACCGCTTCTCGTCCTCTTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 468

AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTGgtatctagag ... ccattatcagGAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGCTCTTGCTAGGCGCATTGCTAAAGTGGGAACCGCTTCTCGTCCTCTTCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 495

AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTGgtatctagag ... ccattatcagGAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGCTCTTGCTAGGCGCATTGCTAAAGTGGGAACCGCTTCTCGTCCTCTTCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 302

AGTAGCGTCTTGAGGGATCTGTCCTCCATGCGACGATTAGTTGTTGCCACCGGAGGTGGTGCTGTCATCCGACCAGTTAACTGgtatctagag ... ccattatcagGAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGCTCTTGCTAGGCGCATTGCTAAAGTGGGAACCGCTTCTCGTCCTCTTCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtcgctttgttttctttgagtcaacagtattgtgacatgtcgttccattatcagGAAATATATGAAGAAGGGCCTATCCGTTTGGTTAGATGTGCCCTTGGATGCTCTTGCTAGGCGCATTGCTAAAGTGGGAACCGCTTCTCGTCCTCTTCTG
                                        tcgttcc  CT-rich tract
      tttgtttt  TA-rich tract