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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgggcgtttgcttggcttattgcgcgtgatcttccacgttgagaggctagacctgtttgtttattttctacattattggccatgctgatgtatctatcgctcgctcacagttgcgtgtatgattgtctgcagGGCGGCCGGTGTGGCATCTATGGAGCCAATTCTCCTGAGTGGGTCATCAGTATGCAG

Basic information

species Zea mays
transcript GRMZM2G152127_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 3
gtatgggcgtttgcttggcttattgcgcgtgatcttccacgttgagaggctagacctgtttgtttattttctacattattggccatgctgatgtatctat-cgctcgctca-cagttgcgtgtatgattgtctgcagGGCGGCCGGTGTGGCATCTATGGAGCCAATTCTCCTGAGTGGGTCATCAGTATGCAG
                        |  ||  ||    || |||    |   |  | || |   | || |     | |  ||     ||| |   |  | |      ||| | | |||||   | ||   |||||||||| || || ||||| || || |||||||| |  ||||||||||| ||||||||||||
------------------------gtacgcaatt---catgttt---gttcatgcttgctctgtgatctgggggagtcgtgaatg-gctaagaaagttgtgtatgtgctaatcggttgctgatttg---gtctgcagGGTGGACGCTGTGGTATTTACGGAGCCAACTGCCCTGAGTGGGTTATCAGTATGCAG
















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|91055766|gb|EB166184.1|EB166184
EST:     ACACCGTGCTCGATGTTGGGTCTGCCATCCGGAGCTGTGGCGTCGGCAAG                         GGCGGCCGGTGTGGCATCTATGGAGCCAATTCTCCTGAGTGGGTCATCAGT
genomic: ACACCGTGCTCGATGTTGGGTCTGCCATCCGGAGCTGTGGCGTCGGCAAGgtatgggcgt ... ttgtctgcagGGCGGCCGGTGTGGCATCTATGGAGCCAATTCTCCTGAGTGGGTCATCAGT
EST: gi|76919428|gb|DV167710.1|DV167710
EST:     ACACCGTGCTCGATGTTGGGTCTGCCATCCGGAGCTGTGGCGTCGGCAAG                         GGCGGCCGGTGTGGCATCTATGGAGCCAATTCTCCTGAGTGGGTCATCAGT
genomic: ACACCGTGCTCGATGTTGGGTCTGCCATCCGGAGCTGTGGCGTCGGCAAGgtatgggcgt ... ttgtctgcagGGCGGCCGGTGTGGCATCTATGGAGCCAATTCTCCTGAGTGGGTCATCAGT
EST: gi|76014959|gb|DT942129.1|DT942129
EST:     ACACCGTGCTCGATGTTGGGTCTGCCATCCGGAGCTGTGGCGTCGGCAAG                         GGCGGCCGGTGTGGCATCTATGGAGCCAATTCTCCTGAGTGGGTCATCAGT
genomic: ACACCGTGCTCGATGTTGGGTCTGCCATCCGGAGCTGTGGCGTCGGCAAGgtatgggcgt ... ttgtctgcagGGCGGCCGGTGTGGCATCTATGGAGCCAATTCTCCTGAGTGGGTCATCAGT
EST: gi|74239653|gb|DT647567.1|DT647567
EST:     ACACCGTGCTCGATGTTGGGTCTGCCATCCGGAGCTGTGGCGTCGGCAAG                         GGCGGCCGGTGTGGCATCTATGGAGCCAATTCTCCTGAGTGGGTCATCAGT
genomic: ACACCGTGCTCGATGTTGGGTCTGCCATCCGGAGCTGTGGCGTCGGCAAGgtatgggcgt ... ttgtctgcagGGCGGCCGGTGTGGCATCTATGGAGCCAATTCTCCTGAGTGGGTCATCAGT
EST: gi|71426983|gb|DR808033.1|DR808033
EST:     ACACCGTGCTCGATGTTGGGTCTGCCATCCGGAGCTGTGGCGTCGGCAAG                         GGCGGCCGGTGTGGCATCTATGGAGCCAATTCTCCTGAGTGGGTCATCAGT
genomic: ACACCGTGCTCGATGTTGGGTCTGCCATCCGGAGCTGTGGCGTCGGCAAGgtatgggcgt ... ttgtctgcagGGCGGCCGGTGTGGCATCTATGGAGCCAATTCTCCTGAGTGGGTCATCAGT
EST: gi|148958182|gb|EC904386.2|EC904386
EST:     ACACCGTGCTCGATGTTGGGTCTGCCATCCGGAGCTGTGGCGTCGGCAAG                         GGCGGCCGGTGTGGCATCTATGGAGCCAATTCTCCTGAGTGGGTCATCAGT
genomic: ACACCGTGCTCGATGTTGGGTCTGCCATCCGGAGCTGTGGCGTCGGCAAGgtatgggcgt ... ttgtctgcagGGCGGCCGGTGTGGCATCTATGGAGCCAATTCTCCTGAGTGGGTCATCAGT
EST: gi|148961536|gb|EE012289.2|EE012289
EST:     ACACCGTGCTCGATGTTGGGTCTGCCATCCGGAGCTGTGGCGTCGGCAAG                         GGCGGCCGGTGTGGCATCTATGGAGCCAATTCTCCTGAGTGGGTCATCAGT
genomic: ACACCGTGCTCGATGTTGGGTCTGCCATCCGGAGCTGTGGCGTCGGCAAGgtatgggcgt ... ttgtctgcagGGCGGCCGGTGTGGCATCTATGGAGCCAATTCTCCTGAGTGGGTCATCAGT
EST: gi|24766862|gb|CA402007.1|CA402007
EST:     CACCGTGCTCGATGTTGGGTCTGCCATCCGGAGCTGTGGCGTCGGTTAG                         GGCGGCCGGTGTGGCATCTATGGAGCCAATTCTCCTGAGTGGGTCATCAGT
genomic: CACCGTGCTCGATGTTGGGTCTGCCATCCGGAGCTGTGGCGTCGGCAAGgtatgggcgt ... ttgtctgcagGGCGGCCGGTGTGGCATCTATGGAGCCAATTCTCCTGAGTGGGTCATCAGT

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: 119

GCTGGCAGCTACACATGGCTGACTTACAAGCAGGTATACGACACCGTGCTCGATGTTGGGTCTGCCATCCGGAGCTGTGGCGTCGGCAAGgtatgggcgt ... ttgtctgcagGGCGGCCGGTGTGGCATCTATGGAGCCAATTCTCCTGAGTGGGTCATCAGTATGCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 51

GCTGGCAGCTACACATGGCTGACTTACAAGCAGGTATACGACACCGTGCTCGATGTTGGGTCTGCCATCCGGAGCTGTGGCGTCGGCAAGgtatgggcgt ... ttgtctgcagGGCGGCCGGTGTGGCATCTATGGAGCCAATTCTCCTGAGTGGGTCATCAGTATGCAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 21

GCTGGCAGCTACACATGGCTGACTTACAAGCAGGTATACGACACCGTGCTCGATGTTGGGTCTGCCATCCGGAGCTGTGGCGTCGGCAAGgtatgggcgt ... ttgtctgcagGGCGGCCGGTGTGGCATCTATGGAGCCAATTCTCCTGAGTGGGTCATCAGTATGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 112

GCTGGCAGCTACACATGGCTGACTTACAAGCAGGTATACGACACCGTGCTCGATGTTGGGTCTGCCATCCGGAGCTGTGGCGTCGGCAAGgtatgggcgt ... ttgtctgcagGGCGGCCGGTGTGGCATCTATGGAGCCAATTCTCCTGAGTGGGTCATCAGTATGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggccatgctgatgtatctatcgctcgctcacagttgcgtgtatgattgtctgcagGGCGGCCGGTGTGGCATCTATGGAGCCAATTCTCCTGAGTGGGTCATCAGTATGCAG
                        cgctcac  putative branch site (score: 112)
             tatctat  TA-rich tract