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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcggtattaactggcagagcacatctatttgttcctttttcgttctatacgctattaagtgaaaagtcaatctcttccttttgctagGCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAA

Basic information

species Zea mays
transcript GRMZM2G060045_T01
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060045_T01 (Zea mays), 3'ss of exon 22
lower sequence: LOC_Os05g01700.1 (Oryza sativa), 3'ss of exon 20
gtcggtattaact--ggcagagcacatctatt----tgttcctttttcgttctatacgctattaagtgaaaagtcaatctcttccttttgctagGCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAA
||| || | ||||  |    ||    |  |||    ||  |  ||  || |  |  | || || | ||||     |    ||   || |   |||| |||||||||||||| |||||||| |||||||| || ||||| ||||| ||
gtcagtgtaaactctgtttcagtctgttaattgcgatgaccagttgccgcttaaatccctttttattgaagttggagctgctgttttcttgcagGCCCGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACGAA

upper sequence: GRMZM2G060045_T01 (Zea mays), 3'ss of exon 22
lower sequence: GLYMA11G38160.1 (Glycine max), 3'ss of exon 24
---------------------------------------------------gtcggtattaactggcagagcacatctatttgttcctttttcgttctatacgctattaagtgaaaagtcaatctcttccttttgctagGCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAA
                                                        |||||  |    ||  ||||     | |   ||| |  |  | | |  | |  | |  ||  |  | ||  |  | ||   |||| || ||||| |||||| | ||||| |||||||||||||||||||| |||||
gtatgtaaatctaatctatattatttttaaaatgagtttgttaaatttgtttaatatattaggtaaaggaagacattagaatat--gtttatgatattcttctatttggattttaacatttaccttatgttctta--agGCACGCTTGTTCTTCCATAAGCCTAAATTTGGTATCCTGGACGAGTGTACCAA

upper sequence: GRMZM2G060045_T01 (Zea mays), 3'ss of exon 22
lower sequence: GLYMA18G02110.1 (Glycine max), 3'ss of exon 25
------------------------------------------------gtcgg-tattaactggcagagcacatctatttgttcctttttcgttctatacgctattaagtgaaaagtcaatctcttccttttgctagGCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAA
                                                || |  |||||  |    ||  ||||     | |   ||| |  |  | | |  | |  | |  ||  |  | ||  |  | ||   |||| || ||||| |||||| | ||||| |||||||||||||||||||| |||||
gtatgtaaatctaatctatattatttttaaaatgggtttgttaaatttgttgaatattaggtataggaagacattagaatat--gtttatgatattcttctatttggattttaacatttaccttgtgttctta--agGCACGCTTGTTCTTCCATAAGCCTAAATTTGGTATCCTGGACGAGTGTACCAA

upper sequence: GRMZM2G060045_T01 (Zea mays), 3'ss of exon 22
lower sequence: PP1S150_142V6.1 (Physcomitrella patens), 3'ss of exon 24
-------------------------------------------------------------------------------------------gtcggtattaactggcagagcacatctat--ttgttcctttttcgttctatacgctattaagtgaaaagtcaatctcttc-cttttgctagGCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAA
                                                                                            |    ||| ||    |  |   || ||   |  |||  |  || | |||    |    | |         |||   ||  || |    |||| ||  | || ||||||||||| |||||||| || || ||||||||||||||
gtaagttcatgaaccggaaattgcgaggttttgtgaggatcgaaaacagatcacgagacttcgaactttaagacgtcttttttgaagatttttgaagatttacgtctaaggttgatttacagtcattcactgatcat-ctaccttcagcaagggttcttactaattagttggctgtcaacagGCACGACTATTCTTCCATCATCCCAAGTTTGGAATTCTTGACGAGTGCACCAA

upper sequence: GRMZM2G060045_T01 (Zea mays), 3'ss of exon 22
lower sequence: EFJ33165 (Selaginella moellendorffii), 3'ss of exon 22
gtcggtattaactggcagagcacatctatttgttcctttttcgttctatacgctattaagtgaaaagtcaatctcttccttttgctagGCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAA
                                      | |  || ||  |  | ||    |        | |      |  ||  |||| ||  | || ||||||||||| |||||||| || |||||||| ||||||||
-------------------------------------gtattattgtaacctgtgtttccaggttttctgacccggaattgctgacagGCGCGACTCTTCTTCCATCATCCGAAGTTTGGAATTCTGGACGAATGCACCAA

upper sequence: GRMZM2G060045_T01 (Zea mays), 3'ss of exon 22
lower sequence: EFJ22756 (Selaginella moellendorffii), 3'ss of exon 23
gtcggtattaactggcagagcacatctatttgttcctttttcgttctatacgctattaagtgaaaagtcaatctcttccttttgctagGCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAA
                                      | |  || ||  |  | ||    |        | |      |  ||  |||| ||  | || ||||||||||| |||||||| || |||||||| ||||||||
-------------------------------------gtattattgtaacctgtgtttccaggttttctgacccgggattgctgacagGCGCGACTCTTCTTCCATCATCCGAAGTTTGGAATTCTGGACGAATGCACCAA

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|60345941|gb|DN212914.1|DN212914
EST:     CAAACTGGGAAGATGTTCTGTCGTTAGGGGAACAACAGAGGCTTGGAATG                         GCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACC
genomic: CAAACTGGGAAGATGTTCTGTCGTTAGGGGAACAACAGAGGCTTGGAATGgtcggtatta ... cttttgctagGCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACC
EST: gi|60351696|gb|DN218669.1|DN218669
EST:     CAAACTGGGAAGATGTTCTGTCGTTAGGGGAACAACAGAGGCTTGGAATG                         GCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACC
genomic: CAAACTGGGAAGATGTTCTGTCGTTAGGGGAACAACAGAGGCTTGGAATGgtcggtatta ... cttttgctagGCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACC
EST: gi|60342685|gb|DN209658.1|DN209658
EST:     CAAACTGGGAAGATGTTCTGTCGTTAGGGGAACAACAGAGGCTTGGAATG                         GCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACC
genomic: CAAACTGGGAAGATGTTCTGTCGTTAGGGGAACAACAGAGGCTTGGAATGgtcggtatta ... cttttgctagGCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACC
EST: gi|32826847|gb|CD966525.1|CD966525
EST:     CAAACTGGGAAGATGTTCTGTCGTTAGGGGAACAACAGAGGCTTGGAATG                         GCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACC
genomic: CAAACTGGGAAGATGTTCTGTCGTTAGGGGAACAACAGAGGCTTGGAATGgtcggtatta ... cttttgctagGCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACC
EST: gi|211295643|gb|FL223363.1|FL223363
EST:     CAAACTGGGAAGATGTTCTGTCGTTAGGGGAACAACAGAGGCTTGGAATG                         GCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACC
genomic: CAAACTGGGAAGATGTTCTGTCGTTAGGGGAACAACAGAGGCTTGGAATGgtcggtatta ... cttttgctagGCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACC
EST: gi|76292548|gb|DV032116.1|DV032116
EST:     CAAACTGGGAAGATGTTCTGTCGTTAGGGGAACAACAGAGGCTTGGAATG                         GCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACC
genomic: CAAACTGGGAAGATGTTCTGTCGTTAGGGGAACAACAGAGGCTTGGAATGgtcggtatta ... cttttgctagGCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACC

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), 45 (downstream exon)
Score: 54

GAATGTTCGGCTGGTGTATCTTCTAGAAAGGGAAGGGTGGGATTCTACACCAAACTGGGAAGATGTTCTGTCGTTAGGGGAACAACAGAGGCTTGGAATGgtcggtatta ... cttttgctagGCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 56

GAATGTTCGGCTGGTGTATCTTCTAGAAAGGGAAGGGTGGGATTCTACACCAAACTGGGAAGATGTTCTGTCGTTAGGGGAACAACAGAGGCTTGGAATGgtcggtatta ... cttttgctagGCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAA


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 20

GAATGTTCGGCTGGTGTATCTTCTAGAAAGGGAAGGGTGGGATTCTACACCAAACTGGGAAGATGTTCTGTCGTTAGGGGAACAACAGAGGCTTGGAATGgtcggtatta ... cttttgctagGCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 114

GAATGTTCGGCTGGTGTATCTTCTAGAAAGGGAAGGGTGGGATTCTACACCAAACTGGGAAGATGTTCTGTCGTTAGGGGAACAACAGAGGCTTGGAATGgtcggtatta ... cttttgctagGCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctttttcgttctatacgctattaagtgaaaagtcaatctcttccttttgctagGCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAA
                                      tctcttccttttgct  CT-rich tract
                    tattaagt  TA-rich tract