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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaggtttcagttcaacagttttttgacatggttctgtgaatgctgctgtgctcattgttgtatgctgatgtttgctagGCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAG

Basic information

species Zea mays
transcript GRMZM2G171469_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171469_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g02850.2 (Oryza sativa), 3'ss of exon 4
gttaggtttcagttcaacagttttttgacatggttctgtgaatgctgctgtgctcattgttgtatgctgatgtttgctagGCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAG
||||| ||| | ||  | | | |||||   | || |  ||  || |  ||| ||||||| |  ||| ||   |||| |||||||| ||| |||| |||||||||||| | |||||||| || |||||||||||| || | ||||  || |||
gttag-ttttacttggata-tattttggttttgtcccatgggtgtttttgttctcattggttcatgatggcatttgttagGCACGGGCAATGTCTACTGATGGGCTCAGACCAGCTTTTTATACAATCAATGGAGTGGTCTATGCAATCCAG
















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|211280348|gb|FL373309.1|FL373309
EST:     CACGACCTAMGCTCTGCTAGTGCTTCTTCTGGGCTGAGATTTACTATCAG                         GCACGTGCAGTGTCGA
genomic: CACGACCTACGCTCTGCTAGTGCT-CTTCTGGGCTGAGATTTACTATCAGgttaggtttc ... tgtttgctagGCACGTGCAGTGTCGA
EST: gi|78108686|gb|DV527104.1|DV527104
EST:     TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAG                         GCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAAT
genomic: TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAGgttaggtttc ... tgtttgctagGCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAAT
EST: gi|32870547|gb|CF010229.1|CF010229
EST:     TCACGACCTACTCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAG                         GCACGTGCAGTGTCG
genomic: TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAGgttaggtttc ... tgtttgctagGCACGTGCAGTGTCG
EST: gi|149017006|gb|EE045660.2|EE045660
EST:     TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAG                         GCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAAT
genomic: TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAGgttaggtttc ... tgtttgctagGCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAAT
EST: gi|211330706|gb|FL425856.1|FL425856
EST:     TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAG                         GCACGTGCAGTGTCGACTGATG
genomic: TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAGgttaggtttc ... tgtttgctagGCACGTGCAGTGTCGACTGATG
EST: gi|91873273|gb|EB403230.1|EB403230
EST:     TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAG                         GCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAAT
genomic: TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAGgttaggtttc ... tgtttgctagGCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAAT
EST: gi|78108178|gb|DV526596.1|DV526596
EST:     TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAG                         GCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAAT
genomic: TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAGgttaggtttc ... tgtttgctagGCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAAT
EST: gi|71322323|gb|DR797838.1|DR797838
EST:     TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAG                         GCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAAT
genomic: TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAGgttaggtttc ... tgtttgctagGCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAAT
EST: gi|50339374|gb|CO534500.1|CO534500
EST:     TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAG                         GCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAAT
genomic: TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAGgttaggtttc ... tgtttgctagGCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAAT
EST: gi|76018861|gb|DT946031.1|DT946031
EST:     TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAG                         GCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAAT
genomic: TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAGgttaggtttc ... tgtttgctagGCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAAT
EST: gi|5895618|gb|AW036864.1|AW036864
EST:     TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAG                         GCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTATACAATCAAT
genomic: TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAGgttaggtttc ... tgtttgctagGCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAAT
EST: gi|74237785|gb|DT645699.1|DT645699
EST:     TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAG                         GCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAAT
genomic: TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAGgttaggtttc ... tgtttgctagGCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAAT
EST: gi|211461108|gb|FL380552.1|FL380552
EST:     TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAG                         GCACGTGCAGTGTCGACTGA
genomic: TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAGgttaggtttc ... tgtttgctagGCACGTGCAGTGTCGACTGA
EST: gi|50333507|gb|CO528633.1|CO528633
EST:     TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAG                         GCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAAT
genomic: TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAGgttaggtttc ... tgtttgctagGCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAAT
EST: gi|71770532|gb|DR968469.1|DR968469
EST:     TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAG                         GCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAAT
genomic: TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAGgttaggtttc ... tgtttgctagGCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAAT
EST: gi|149075806|gb|EE164341.2|EE164341
EST:     TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAG                         GCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAAT
genomic: TCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAGgttaggtttc ... tgtttgctagGCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAAT

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), 47 (downstream exon)
Score: 46

ATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAGgttaggtttc ... tgtttgctagGCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 73

ATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAGgttaggtttc ... tgtttgctagGCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 54

ATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAGgttaggtttc ... tgtttgctagGCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

ATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAGgttaggtttc ... tgtttgctagGCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacatggttctgtgaatgctgctgtgctcattgttgtatgctgatgtttgctagGCACGTGCAGTGTCGACTGATGGGCTCCGGCCAGCTTTCTACACAATCAATGGAATGATATATGTCATTCAG
                                       tgctgat  putative branch site (score: 105)