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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaacattttaccccctcgtacacgtctctgtgaatgatgtttttacattaatttggccatcttttattgatgtaatccctttcccttggactctccctgcagCTTGCTGCAGTGGCAGCACTGTGTGTGCAATACGAAGCAGAGTTCAGGCCCAACATGAGCATTGTTGTGAAGGCGCTTTCGCCTCTCCTTCAACAAAGAC

Basic information

species Zea mays
transcript GRMZM2G071877_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G071877_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g62700.1 (Oryza sativa), 3'ss of exon 7
------------------------gtcaacattttaccccctcgtacacgt-ctctg-tgaatgatgtttttacattaatt----tggccatcttttattgatgtaatccctttcccttggact----ctccctgcagCTTGCTGCAGTGGCAGCACTGTGTGTGCAATACGAAGCAGAGTTCAGGCCCAACATGAGCATTGTTGTGAAGGCGCTTTCGCCTCTCCTTCAACAAAGAC
                            |||    |||| | | |||||   || || || |     ||||||||| | ||    | ||  || |  | | |||| ||     |    | |  |     |  |||||||||||||| |||||||| || ||||| ||||||||||||||||||||||||||||||||||||||||| |||||||| || ||||| |||||||||| ||
gtcagtctctcgtctctctctctctctcacaccc-acccacacatacacacactatgatgcacatgctttttacatcatttggagtagcagtcctgaaataatgtcatgttgatgtacttggttgcacttatctgcagCTTGCTGCGGTGGCAGCTCTTTGTGTCCAATACGAAGCAGAGTTCAGGCCCAACATGAGCATTGTTGTCAAGGCGCTCTCTCCTCTGCTTCAACAAAAAC

upper sequence: GRMZM2G071877_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA20G38980.1 (Glycine max), 3'ss of exon 8
--------gtcaacattttaccccctc---gtacacgtctctgtgaatgatgtttttac--attaat-------------ttggccatc--ttttattgatgtaatcc-ctttcccttggactctccctgcagCTTGCTGCAGTGGCAGCACTGTGTGTGCAATACGAAGCAGAGTTCAGGCCCAACATGAGCATTGTTGTGAAGGCGCTTTCGCCTCTCCTTCAACAAAGAC
         || |  | | || ||      || ||||    ||||||     | || ||  || |||             ||||   ||  |||||| | ||  ||   |  | |||     |  || |||||||||  || || || |||||||| ||||| || ||||| ||||| ||||| || |||||||||||||| || || ||    || || ||  |        
gtatctatttctatttctcactcctcttaagtgcacgcacatgtgaaaagactattgactcatgaataaagttctggtgcttggatctccattttatggttgacattaaccgtgcctactgttgaccgtgcagCTTGGAGCTGTTGCGGCACTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCAAATATGAGCATTGTTGTTAAAGCACTCCAACCACTTCTGAAGTCTCCTG

upper sequence: GRMZM2G071877_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT3G59350.3 (Arabidopsis thaliana), 3'ss of exon 5
gtcaacattttaccccctcgtacacgtctctgtgaatgatgtttttacattaatttggccatcttttattgatgtaatccctttc-ccttggactctccctgcagCTTGCTGCAGTGGCAGCACTGTGTGTGCAATACGAAGCAGAGTTCAGGCCCAACATGAGCATTGTTGTGAAGGCGCTTTCGCCTCTCCTTCAACAAAGAC
||  |   || | |   | |   ||   |   |  || |    |    |   | ||    | |  | |       |  |  |||| |||||  ||  | || ||||| |||||||| |||||| ||||||||||||| ||| ||||||| ||||| |||||||||||||| || || || |||   ||  |  |      |  | 
gtataagcttcatctttttg---acagtttaatctataacccctgcgaaaccactttcaaaacgctaaccataaaatactgtttcgccttgttcttgcgcttcagCTCGCTGCAGTAGCAGCATTGTGTGTGCAATATGAATCAGAGTTTAGGCCAAACATGAGCATTGTGGTAAAAGCTCTTCAACCATTGTTGAGGTCATCAA

upper sequence: GRMZM2G071877_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT2G43230.1 (Arabidopsis thaliana), 3'ss of exon 6
gtcaacattttaccccctcgtacacgtctctgtgaatgatgtttttacattaatttggccatcttttattgatgtaatccctttcccttggactctccctgcagCTTGCTGCAGTGGCAGCACTGTGTGTGCAATACGAAGCAGAGTTCAGGCCCAACATGAGCATTGTTGTGAAGGCGCTTTCGCCTCTCCTTCAACAAAGAC
                   | |||      |   | | || |   ||  |  | | | ||    ||    | |  |||   | |   || ||   |   | |||||||| || || |||||  ||||||||||||||||||||||||| ||||| |||||||||||||| || || || |||   || ||| |      |  | 
--------------gtaatgaacagaaacttcctagtcatttaaataactctagtggaccccacttacaagctaaaatgtgtgt---tttgatggtaaatacagCTTGCAGCGGTTGCAGCGTTGTGTGTGCAATACGAAGCAGAGTTTAGGCCAAACATGAGCATTGTAGTAAAAGCTCTTCAACCGCTCTTGAGGTCAGCAA

upper sequence: GRMZM2G071877_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv05s0124g00360.t01 (Vitis vinifera), 3'ss of exon 7
gtcaacattttaccccctcgtacacgtctctgtgaatgatgtttttacattaatttggccatcttttattgatgtaatccctttcccttggactctccctgcagCTTGCTGCAGTGGCAGCACTGTGTGTGCAATACGAAGCAGAGTTCAGGCCCAACATGAGCATTGTTGTGAAGGCGCTTTCGCCTCTCCTTCAACAAAGAC--
     |  ||| || |    |     ||||| |             ||| | |       ||   |  | | |   | | || |   ||||        ||||||| || || ||||||||| | ||||| || |||||||| |||||| |||| || |||||||| ||||||||||| ||    || ||  || ||      |  
---gtctctttgcctctctctctctctctctctctcacccacacacacactcacagaaaaataactagtagct---aactctgtgaattgg-tgggtgatgcagCTGGCAGCTGTGGCAGCATTATGTGTTCAGTACGAAGCTGAGTTCCGGCCAAATATGAGCATCGTTGTGAAGGCTCTCCAACCGCT--TTTAAAGGCTGCTG

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|5714227|gb|AI944212.1|AI944212
EST:     GTGTAGATCCCAGGTTGAAGGGAGAATATCCTCCAAAGGGAGTCGGTAAG                         CTTGCTGCAGTGGCAGCACTGTGTGTGCAATNCGAAGCAGAGTTCAGGCCC
genomic: GTGTAGATCCCAGGTTGAAGGGAGAATATCCTCCAAAGGGAGTCGCTAAGgtcaacattt ... ctccctgcagCTTGCTGCAGTGGCAGCACTGTGTGTGCAATACGAAGCAGAGTTCAGGCCC
EST: gi|6020326|gb|AW065254.1|AW065254
EST:     GTGTAGATCCCAGGTTGAAGGGAGAATATCCTCCAAAGGGAGTCGCTAAG                         CTTGCTGCAG-GGCAGCAC
genomic: GTGTAGATCCCAGGTTGAAGGGAGAATATCCTCCAAAGGGAGTCGCTAAGgtcaacattt ... ctccctgcagCTTGCTGCAGTGGCAGCAC
EST: gi|6227256|gb|AW155855.1|AW155855
EST:     GTGTAGATCCCAGGTTGAAGGGAGAATATCCTCCAAAGGGAGTCGCTAAG                         CTTGCTGCAGTGGCAGCACTGTGTGTGCAATACGAAGCAGAGTTCAGGCCC
genomic: GTGTAGATCCCAGGTTGAAGGGAGAATATCCTCCAAAGGGAGTCGCTAAGgtcaacattt ... ctccctgcagCTTGCTGCAGTGGCAGCACTGTGTGTGCAATACGAAGCAGAGTTCAGGCCC
EST: gi|60348834|gb|DN215807.1|DN215807
EST:     GTGTAGATCCCAGGTTGAAGGGAGAATATCCTCCAAAGGGAGTCGCTAAG                         CTTGCTGCAGTGGCAGCACTGTGTGTGCAATACGAAGCAGAGTTCAGGCCC
genomic: GTGTAGATCCCAGGTTGAAGGGAGAATATCCTCCAAAGGGAGTCGCTAAGgtcaacattt ... ctccctgcagCTTGCTGCAGTGGCAGCACTGTGTGTGCAATACGAAGCAGAGTTCAGGCCC
EST: gi|31351642|gb|CD435999.1|CD435999
EST:     GTGTAGATCCCAGGTTGAAGGGAGAATATCCTCCAAAGGGAGTCGCTAAG                         CTTGCTGCAGTGGCAGCACTGTGTGTGCAATACGAAGCAGAGTTCAGGCCC
genomic: GTGTAGATCCCAGGTTGAAGGGAGAATATCCTCCAAAGGGAGTCGCTAAGgtcaacattt ... ctccctgcagCTTGCTGCAGTGGCAGCACTGTGTGTGCAATACGAAGCAGAGTTCAGGCCC
EST: gi|211301860|gb|FL439774.1|FL439774
EST:     GTGTAGATCCCAGGTTGAAGGGAGAATATCCTCCAAAGGGAGTCGCTAAG                         CTTGCTGCAGTGGCAGCACTGTGTGTGCAATACGAAGCAGAGTTCAGGCCC
genomic: GTGTAGATCCCAGGTTGAAGGGAGAATATCCTCCAAAGGGAGTCGCTAAGgtcaacattt ... ctccctgcagCTTGCTGCAGTGGCAGCACTGTGTGTGCAATACGAAGCAGAGTTCAGGCCC
EST: gi|5860445|gb|AW011667.1|AW011667
EST:     GTGTAGATCCCAGGTTGAAGGGAGAATATCCTCCAAAGGGAGTCGCTAAG                         CTTGCTGCAGTGGCAGCACTGTGTGTGCAATACGAAGCAGAGTTCAGGCCC
genomic: GTGTAGATCCCAGGTTGAAGGGAGAATATCCTCCAAAGGGAGTCGCTAAGgtcaacattt ... ctccctgcagCTTGCTGCAGTGGCAGCACTGTGTGTGCAATACGAAGCAGAGTTCAGGCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatttggccatcttttattgatgtaatccctttcccttggactctccctgcagCTTGCTGCAGTGGCAGCACTGTGTGTGCAATACGAAGCAGAGTTCAGGCCCAACATGAGCATTGTTGTGAAGGCGCTTTCGCCTCTCCTTCAACAAAGAC
                 tattgat  putative branch site (score: 3)
                            tccctttcccttggac  putative PPT
              ttttattgatgtaat  TA-rich tract