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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcgaactttatcagtccattgtcccaatggcttattgctttacatgaatacggggtagttagttttttcataacaaacacaaacctgctgccttttgcataccaagctctgtctcttttattgtaaaaccagGTTATTGGCCCCTATCGGTCGGGCAAATCTTTTCTTCTCAACCAACTTCTCTCCCTATCATGTGACAATG

Basic information

species Zea mays
transcript GRMZM2G030138_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030138_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g08400.1 (Oryza sativa), 3'ss of exon 2
gtatgttcgaactttatcagtccattgtcccaatggcttattgctttacatgaatacggggtagttagttttttcataacaaacacaaacctgctgccttt---------------tgcataccaagctctgtctcttttattgtaaaaccagGTTATTGGCCCCTATCGGTCGGGCAAATCTTTTCTTCTCAACCAACTTCTCTCCCTATCATGTGACAATG
                         |||   |||||  | | |||  |||| |||||  | ||||| | |||| |  ||| ||  | ||    ||   |||               ||||| |  || | | | ||| | | | | ||| ||||||||||| || ||||| || || ||||||||||||||||| || |||||||||||| ||||  | || |
----------------------gtatgtttaaatgggctgtagctc-acataaatacctgatagtttgcttttcc-caactaatgccaaggcactatatttatttctttgtcgtggtgcatgctgagttatatgtctctgactctcaaatcagGTTATTGGGCCATATCGATCTGGAAAATCTTTTCTTCTCAATCAGCTTCTCTCCCTAACATGCAATAAAG
















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|76924745|gb|DV170113.1|DV170113
EST:     AAGGTCTGGAAGCAATTCAGAGGATCAGAACTCCAATAGCTGCTGTTTCT                         GTTATTGGCCCCTATCGGTCGGGCAAATCTTTTCTTCTCAACCAACTTCTC
genomic: AAGGTCTGGAAGCAATTCAGAGGATCAGAACTCCAATAGCTGCTGTTTCTgtatgttcga ... gtaaaaccagGTTATTGGCCCCTATCGGTCGGGCAAATCTTTTCTTCTCAACCAACTTCTC
EST: gi|89763546|gb|DY690690.1|DY690690
EST:     AAGGTCTGGAAGCAATTCAGAGGATCAGAACTCCAATAGCTGCTGTTTCT                         GTTATTGGCCCCTATCGGTCGGGCAAATCTTTTCTTCTCAACCAACTTCTC
genomic: AAGGTCTGGAAGCAATTCAGAGGATCAGAACTCCAATAGCTGCTGTTTCTgtatgttcga ... gtaaaaccagGTTATTGGCCCCTATCGGTCGGGCAAATCTTTTCTTCTCAACCAACTTCTC
EST: gi|71449828|gb|DR830878.1|DR830878
EST:     AAGGTCTGGAAGCAATTCAGAGGATCAGAACTCCAATAGCTGCTGTTTCT                         GTTATTGGCCCCTATCGGTCGGGCAAATCTTTTCTTCTCCACCAACTTCTC
genomic: AAGGTCTGGAAGCAATTCAGAGGATCAGAACTCCAATAGCTGCTGTTTCTgtatgttcga ... gtaaaaccagGTTATTGGCCCCTATCGGTCGGGCAAATCTTTTCTTCTCAACCAACTTCTC

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: 8 (upstream exon), 42 (downstream exon)
Score: 2

TCCAATAGTGAAGCCAGACTACGGGCACACGAAACTCCAACTCGCAAAAGAAGGTCTGGAAGCAATTCAGAGGATCAGAACTCCAATAGCTGCTGTTTCTgtatgttcga ... gtaaaaccagGTTATTGGCCCCTATCGGTCGGGCAAATCTTTTCTTCTCAACCAACTTCTCTCCCTATCATGTGACAATG


Block sizes: 32 (upstream exon), 18 (downstream exon)
Score: 1

TCCAATAGTGAAGCCAGACTACGGGCACACGAAACTCCAACTCGCAAAAGAAGGTCTGGAAGCAATTCAGAGGATCAGAACTCCAATAGCTGCTGTTTCTgtatgttcga ... gtaaaaccagGTTATTGGCCCCTATCGGTCGGGCAAATCTTTTCTTCTCAACCAACTTCTCTCCCTATCATGTGACAATG


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 3

TCCAATAGTGAAGCCAGACTACGGGCACACGAAACTCCAACTCGCAAAAGAAGGTCTGGAAGCAATTCAGAGGATCAGAACTCCAATAGCTGCTGTTTCTgtatgttcga ... gtaaaaccagGTTATTGGCCCCTATCGGTCGGGCAAATCTTTTCTTCTCAACCAACTTCTCTCCCTATCATGTGACAATG


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 9

TCCAATAGTGAAGCCAGACTACGGGCACACGAAACTCCAACTCGCAAAAGAAGGTCTGGAAGCAATTCAGAGGATCAGAACTCCAATAGCTGCTGTTTCTgtatgttcga ... gtaaaaccagGTTATTGGCCCCTATCGGTCGGGCAAATCTTTTCTTCTCAACCAACTTCTCTCCCTATCATGTGACAATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacaaacctgctgccttttgcataccaagctctgtctcttttattgtaaaaccagGTTATTGGCCCCTATCGGTCGGGCAAATCTTTTCTTCTCAACCAACTTCTCTCCCTATCATGTGACAATG
                                    tcttttattgtaaaa  TA-rich tract