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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatatttagttttgctgggcaaactttcagtataaacacagtgcatcaaaattaatgttggtgctgttcttgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTCACAAACATGAGCCTTGGAAAGGTTGCAGTGTCATTTACACATACTATAA

Basic information

species Zea mays
transcript GRMZM2G047404_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047404_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g12600.2 (Oryza sativa), 3'ss of exon 2
gtgaatatttagttttgctgggca---------aactttcagtataaacacagtgcatca--aaattaa-tgttggtgctgttcttgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTCACAAACATGAGCCTTGGAAAGGTTGCAGTGTCATTTACACATACTATAA
|| | ||| |   | |    |  |         ||| |||  || | |   | ||||  |  ||   || | |||   |||| ||| ||||  |||||   |||||||||||||| ||||| ||||| |||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| |
gtaattatatttctctataagatacatcgtgacaacattcgatacacatgtattgcactatgaagccaactattgtaactgtccttatttc--agCTTGCTGCTATCCTTCCTCTCGCTATGGTCCACACCATGGGCAATCTTTTCACGAACATGAGCCTTGGAAAGGTTGCAGTGTCATTTACACATACTATCA

upper sequence: GRMZM2G047404_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ27053 (Selaginella moellendorffii), 3'ss of exon 2
gtgaatatttagttttgctgggcaaactttca---gtataaacacagtgcatcaaaattaatgttggtgctgttcttgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTCACAAACATGAGCCTTGGAAAGGTTGCAGTGTCATTTACACATACTATAA
           || | |  |   ||| | ||    || |  |   ||    ||||| ||        ||   || ||  |||  || |  |||| ||| | || || ||  | || || |||||||| ||||| || || ||||||||||||||||||||||| ||||| ||||| || || || |
-----------gtatcgtcgtagaaattgtcgtttgtgtcgatcgagcatctcaaacttt-------tgtccttgtttcttcgtagGTGGTCGCGATCTTGCCGCTGGCATTGGTGCACACCATGGGGAATCTCTTTACCAACATGAGCCTTGGAAAGGTTGCGGTGTCGTTTACTCACACAATCA

upper sequence: GRMZM2G047404_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ05868 (Selaginella moellendorffii), 3'ss of exon 2
gtgaatatttagttttgctgggcaaactttcagt-ataaacacagtgcatcaaaattaatgttggtgctgttcttgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTCACAAACATGAGCCTTGGAAAGGTTGCAGTGTCATTTACACATACTATAA
           || | |  |   ||| | ||  |  |  | |  | |||||   |  ||| |||    ||||     |||  || |  |||| ||| | || || ||  | || || |||||||| ||||| || || ||||||||||||||||||||||| ||||||||||| || || || |
-----------gtatcgtcgtagaaattgtcgtttgtgtagatcgagcatctctaaaaattttgtccttgtttc---ttcgtagGTGGTCGCGATCTTGCCGCTGGCATTGGTGCACACCATGGGGAATCTCTTTACCAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACTCACACAATCA

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|211421923|gb|FL203903.1|FL203903
EST:     CTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAG                         CTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTC
genomic: CTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTC
EST: gi|37376326|gb|CF624676.1|CF624676
EST:     TCATGTGGATCACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAG                         CTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTC
genomic: TCATGTGGATCACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTC
EST: gi|40336776|gb|CK370846.1|CK370846
EST:     TCATGTGGATCACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAG                         CTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTC
genomic: TCATGTGGATCACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTC
EST: gi|148990723|gb|EE032129.2|EE032129
EST:     TCATGTGGATCACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAG                         CTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTC
genomic: TCATGTGGATCACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTC
EST: gi|50325876|gb|CO521002.1|CO521002
EST:     TCATGTGGATCACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAG                         CTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTC
genomic: TCATGTGGATCACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTC
EST: gi|22521317|gb|BU080128.1|BU080128
EST:     TCATGTGGATTACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAG                         CTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTC
genomic: TCATGTGGATCACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTC
EST: gi|76281901|gb|DV021469.1|DV021469
EST:     TCATGTGGATCACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAG                         CTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTC
genomic: TCATGTGGATCACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTC
EST: gi|88753541|gb|DY537682.1|DY537682
EST:     TCATGTGGATCACTGGTATTCATAAAAGGCCAAAGATTTCGGGTGCCCAG                         CTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTC
genomic: TCATGTGGATCACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTC
EST: gi|21891481|gb|BQ744694.1|BQ744694
EST:     TCATGTGGATTACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAG                         CTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTC
genomic: TCATGTGGATCACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTC
EST: gi|87156219|gb|DY401008.1|DY401008
EST:     TCATGTGGATTACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAG                         CTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGGAATCTTT
genomic: TCATGTGGATCACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTT
EST: gi|26559240|gb|CA831475.1|CA831475
EST:     TCATGTGGATTACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAG                         CTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGC
genomic: TCATGTGGATCACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGC
EST: gi|6973548|gb|AW438284.1|AW438284
EST:     TCATGTGGATCACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAG                         CTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTC
genomic: TCATGTGGATCACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTC

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: 206

TATAAACATCACAACGGTGCAGTTTGCTGTTGGAAGTGCCATTGCTTTGTTCATGTGGATCACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTCACAAACATGAGCCTTGGAAAGGTTGCAGTGTCATTTACACATACTATAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 162

TATAAACATCACAACGGTGCAGTTTGCTGTTGGAAGTGCCATTGCTTTGTTCATGTGGATCACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTCACAAACATGAGCCTTGGAAAGGTTGCAGTGTCATTTACACATACTATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 196

TATAAACATCACAACGGTGCAGTTTGCTGTTGGAAGTGCCATTGCTTTGTTCATGTGGATCACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTCACAAACATGAGCCTTGGAAAGGTTGCAGTGTCATTTACACATACTATAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 399

TATAAACATCACAACGGTGCAGTTTGCTGTTGGAAGTGCCATTGCTTTGTTCATGTGGATCACTGGTATCCATAAAAGGCCAAAGATTTCGGGTGCCCAGgtgaatattt ... tgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTCACAAACATGAGCCTTGGAAAGGTTGCAGTGTCATTTACACATACTATAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagtataaacacagtgcatcaaaattaatgttggtgctgttcttgtttcccagCTTTTCGCTATCCTTCCTCTAGCTATTGTCCATACCATGGGCAATCTTTTCACAAACATGAGCCTTGGAAAGGTTGCAGTGTCATTTACACATACTATAA
                        aattaat  putative branch site (score: 399)
                                      ctgttcttgtttccc  putative PPT
                   atcaaaattaatgtt  TA-rich tract