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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtacgagacttagcacacaggcagcagcagcgttctatatctcagttgcttgcttctgagttctgacacactgtactgtgggtttcagGTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGCTAGTGCGCGAGTGGGTACAGTTCTGCATCTTCATGTACATTGG

Basic information

species Zea mays
transcript GRMZM5G866432_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G866432_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g48570.1 (Oryza sativa), 3'ss of exon 5
gtacgtacgagacttagcacacaggcagcagcagcgttct---atatctcagttgctt-------gcttctgagttctgacacactgtactgtgggtttcagGTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGCTAGTGCGCGAGTGGGTACAGTTCTGCATCTTCATGTACATTGG
    ||| ||      ||| ||     |||   | |||||   ||   |   ||| ||       ||| |||| |||||| |       |||||   ||||||| |||||||||||||| || || |||||||||||||||||||||||  | ||||| || ||||||||||| ||||| |||||||| |||||
----gtatgacttaatgcatacgtatggcatt-gtgttctggtatgatttgtttggtttggcagcgctcctgaattctgatagtgccatctgtgc-cttcagGTGTACATGAGGGCTGATGATACACCAGATAACTACTGGTTTCGCGTATTGGTGCGTGAATGGGTACAGTTTTGCATATTCATGTATATTGG

upper sequence: GRMZM5G866432_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g27795.1 (Oryza sativa), 3'ss of exon 4
---gtacgtacgagacttagcacacaggcagcagcagcgttctatatctcagttgcttgcttctgagttctgacacactgtactgtgggtttcagGTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGCTAGTGCGCGAGTGGGTACAGTTCTGCATCTTCATGTACATTGG
     || || |     ||   ||  |    | ||   | ||| | |          |||| |||| |||| | |       |||||  ||| |||| |||||||||||||| |  || |||||||||||||||||||| ||  | ||||| || ||||||||||| ||||| |||||||| |||||
gtatgacttatgcatactatggcattgtgttctgctatgatctgtttggtttggcagtgctcctgaattctaatagtgccatctgtgccttt-agGTGTACATGAGGGCTGATGGTACACCAGATAACTACTGGTTTCGTGTATTGGTGCGTGAATGGGTACAGTTTTGCATATTCATGTATATTGG
















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|149112019|gb|EE191181.2|EE191181
EST:     GAGGTTTCAGGGAACGATGCAGGTGGCCGCAGTGGCATTCATCATG                         GTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGCTA
genomic: GAGGTTTCAGGGAACGATGCAGGTGGCCGCAGTGGCATTCATCATGgtacgtacga ... tgggtttcagGTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGCTA
EST: gi|116818727|gb|EC861775.1|EC861775
EST:     GAGGTTTCA-GGAACGATGCAGGTGGCCGCAGTGGCATTCATCATG                         GTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGCTA
genomic: GAGGTTTCAGGGAACGATGCAGGTGGCCGCAGTGGCATTCATCATGgtacgtacga ... tgggtttcagGTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGCTA
EST: gi|149112945|gb|EE191470.2|EE191470
EST:     GAGGTTTCAGGGAACGATGCAGGTGGCCGCAGTGGCATTCATCATG                         GTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGCTA
genomic: GAGGTTTCAGGGAACGATGCAGGTGGCCGCAGTGGCATTCATCATGgtacgtacga ... tgggtttcagGTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGCTA
EST: gi|148962391|gb|EE013237.2|EE013237
EST:     GAGGTTTCAGGGAACGATGCAGGTGGCCGCAGTGGCATTCATCATG                         GTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTT
genomic: GAGGTTTCAGGGAACGATGCAGGTGGCCGCAGTGGCATTCATCATGgtacgtacga ... tgggtttcagGTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTT
EST: gi|148961851|gb|EE012634.2|EE012634
EST:     GAGGTTTCAGGGAACGATGCAGGTGGCCGCAGTGGCATTCATCATG                         GTATACATGAAGGCTGACGACACCCCAGATAACTACTGGTTT
genomic: GAGGTTTCAGGGAACGATGCAGGTGGCCGCAGTGGCATTCATCATGgtacgtacga ... tgggtttcagGTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTT
EST: gi|148931606|gb|EC874722.2|EC874722
EST:     GAGGTTTCAGGGAACGATGCAGGTGGCCGCAGTGGCATTCATCATG                         GTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGCTA
genomic: GAGGTTTCAGGGAACGATGCAGGTGGCCGCAGTGGCATTCATCATGgtacgtacga ... tgggtttcagGTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGCTA
EST: gi|148947485|gb|EC892931.2|EC892931
EST:     GAGGTTTCAGGGAACGATGCAGGTGGCCGCAGTGGCATTCATCATG                         GTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGCTA
genomic: GAGGTTTCAGGGAACGATGCAGGTGGCCGCAGTGGCATTCATCATGgtacgtacga ... tgggtttcagGTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGCTA
EST: gi|149044668|gb|EE047641.2|EE047641
EST:     AGAGGTTTCAGGGAACGATGCAGGTGGCCGCAGTGGCATTCATCATG                         GTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGCTA
genomic: AGAGGTTTCAGGGAACGATGCAGGTGGCCGCAGTGGCATTCATCATGgtacgtacga ... tgggtttcagGTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGCTA
EST: gi|149044669|gb|EE047642.2|EE047642
EST:     GAGGTTTCAGGGAACGATGCAGGTGGCCGCAGTGGCATTCATCATG                         GTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGCTA
genomic: GAGGTTTCAGGGAACGATGCAGGTGGCCGCAGTGGCATTCATCATGgtacgtacga ... tgggtttcagGTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGCTA
EST: gi|148962390|gb|EE013236.2|EE013236
EST:     GAGGTTTCAGGGAACGATGCAGGTGGCGGCAGTGGCATTCATCATG                         GTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGCTA
genomic: GAGGTTTCAGGGAACGATGCAGGTGGCCGCAGTGGCATTCATCATGgtacgtacga ... tgggtttcagGTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGCTA
EST: gi|148944915|gb|EC890074.2|EC890074
EST:     GAGGTTTCAGGGAACGATGCAGGTGGCCGCAGTGGCATTCATCATG                         GTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGCTA
genomic: GAGGTTTCAGGGAACGATGCAGGTGGCCGCAGTGGCATTCATCATGgtacgtacga ... tgggtttcagGTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGCTA
EST: gi|149083349|gb|EE172648.2|EE172648
EST:     GAGGTTTCAGGGAACGATGCAGGTGGCCGCAGTGGCATTCATCATG                         GTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGC
genomic: GAGGTTTCAGGGAACGATGCAGGTGGCCGCAGTGGCATTCATCATGgtacgtacga ... tgggtttcagGTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGC
EST: gi|149096166|gb|EE181863.2|EE181863
EST:     GAGGTTTCAGGGAACGATGCAGGTGGCCGCAGTGGCATTCATCATG                         GTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGCTA
genomic: GAGGTTTCAGGGAACGATGCAGGTGGCCGCAGTGGCATTCATCATGgtacgtacga ... tgggtttcagGTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGCTA

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: 11 (upstream exon), 39 (downstream exon)
Score: 1

GAGGTTTCAGGGAACGATGCAGGTGGCCGCAGTGGCATTCATCATGgtacgtacga ... tgggtttcagGTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGCTAGTGCGCGAGTGGGTACAGTTCTGCATCTTCATGTACATTGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 8

GAGGTTTCAGGGAACGATGCAGGTGGCCGCAGTGGCATTCATCATGgtacgtacga ... tgggtttcagGTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGCTAGTGCGCGAGTGGGTACAGTTCTGCATCTTCATGTACATTGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 194

GAGGTTTCAGGGAACGATGCAGGTGGCCGCAGTGGCATTCATCATGgtacgtacga ... tgggtttcagGTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGCTAGTGCGCGAGTGGGTACAGTTCTGCATCTTCATGTACATTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctatatctcagttgcttgcttctgagttctgacacactgtactgtgggtttcagGTATACATGAGGGCTGACGACACGCCAGATAACTACTGGTTTCGCGTGCTAGTGCGCGAGTGGGTACAGTTCTGCATCTTCATGTACATTGG
                           ttctgac  putative branch site (score: 194)