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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcaatgtttaattattgtgctttgttcatacttcacagtataaatacttaagatacgtcaagttatgctatccatgtgctagccttatttactatattccaattaatttgttgctactctatgtttactaagtagttttttggttaaatttttctgtagGGAGTTTTTGGTTGATCTGATGGCTGCTCCTGGTGCTCTTATTCCAGCAGATATCTTAAGTTGGAAAGGCAATTCGTTAAATTCTAATCGAAAACTCGGC

Basic information

species Zea mays
transcript GRMZM2G044180_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044180_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g06410.1 (Oryza sativa), 3'ss of exon 3
gtatcaatgtttaattattgtgctttgttcatacttcacagtataaatacttaagatacgtcaagttatgctatccatgtgctagccttattt--actatattcc-aattaatttg---ttgctactctatgtttactaagtagttttttggttaaatttttctgtagGGAGTTTTTGGTTGATCTGATGGCTGCTCCTGGTGCTCTTATTCCAGCAGATATCTTAAGTTGGAAAGGCAATTCGTTAAATTCTAATCGAAAACTCGGC
                                                                 ||||  ||| | | ||||| | || |||  | ||||||   || |||||||   ||||| |  ||  ||| |||||| | ||| ||      | ||| || |||||||||||||||||||| ||||||||||| ||| ||||||||||| ||||| ||||||||||||| ||||| || ||||||||||||  || ||||  |
----------------------------------------------------------------tttat-ttattcgtctgctacctttgtttcaaatatatttttaaataatttggtattgctgccttacattttctaagtgggtttatgtgc---tgtttttgcagGGAGTTTTTGGTTGATCTCATGGCTGCTCCCGGTACTCTTATTCCATCAGATGTCTTAAGTTGGAAGGGCAACTCATTAAATTCTAATGCAAGACTCACC

upper sequence: GRMZM2G044180_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA10G30070.1 (Glycine max), 3'ss of exon 4
gtatcaatgttta-attattgtgctttgttcatacttcacagtataaatacttaagata-cgtcaagttatgctatccatgtgctagccttatt--tactatattccaattaatttgttgctactct--atgtttactaagtagttttttggtta---aatttttctgtagGGAGTTTTTGGTTGATCTGATGGCTGCTCCTGGTGCTCTTATTCCAGCAGATATCTTAAGTTGGAAAGGCAATTCGTTAAATTCT---AATCGAAAACTCGGC
||       |||| ||  ||||  |||  |  || ||   | | ||   | ||| |  | | |    |     | |  |||        | |||  | | ||  |   ||   | |     ||| |   | |||||    || ||  |    |     | | |   |  |||||||||||||||||||| ||||||||||| ||  | ||||| ||||| ||||| |||||    || |  | | | || ||  ||   ||||  ||  |    
gttaaggcttttacatctttgtatttttcttgtatttgttaatttactaatttatgtaatcattggatacaaatttatatgcatggaaatgattgatgcgatcattggatatctctaagtttacccggaaagtttatgttgtggtactgacatctcctactctgctttcagGGAGTTTTTGGTTGATCTCATGGCTGCTCCAGGGACACTTATCCCAGCTGATATTTTAAGCACCAAGGATAGTGCCTTTAAGCCTTACAATCCCAAGATT---

upper sequence: GRMZM2G044180_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA20G37330.1 (Glycine max), 3'ss of exon 3
gtatcaatgttta-attattgtgctttgttcatacttcacagtataaatacttaag-atacgtcaagttatgctatccatgtgctagccttatttactatattccaattaat---ttgttgctactctatgtttactaagtagttttttggt-------taaatttttctgt---------agGGAGTTTTTGGTTGATCTGATGGCTGCTCCTGGTGCTCTTATTCCAGCAGATATCTTAAGTTGGAAAGGCAATTCGTTAAATTCT---AATCGAAAACTCGGC
||       |||| ||  ||||  |||  |  || ||   | | ||   | ||| | || | |     |||  | | ||||     |   | ||    ||  |  |   |||   | | ||   || || ||| ||  || |  ||| || |       | |  | | ||           |||||||||||||||||||| ||||||||||| ||  | ||||| ||||| ||||| |||||    || |  | | | || || |||   ||||  ||  |    
gttaaggcttttacatctttgtatttttcttgtatttgttaatttactaatttatgtatgcatgtgtatatcatgtgcatgcctatgtactcttgtaaatggttgaggcaatcattggatgtctctataagttcacccagaaagtttatgttgtggtactgacgtctcctactctgctttcagGGAGTTTTTGGTTGATCTCATGGCTGCTCCAGGGACACTTATCCCAGCTGATATTTTAAGCACCAAGGATAGTGCCTTTAAGTCTTACAATCCCAAGATT---

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|149102684|gb|EE288035.2|EE288035
EST:     GGTGGTGATGACGACGATGCTATAAACATAATTAAGATGGACAATGAAAG                         GGAGTTTTTGGTTGATCTGATGGCTGCTCCTGGTGCTCTTATTCCAGCAGA
genomic: GGTGGTGATGACGACGATGCTATAAACATAATTAAGATGGACAATGAAAGgtatcaatgt ... ttttctgtagGGAGTTTTTGGTTGATCTGATGGCTGCTCCTGGTGCTCTTATTCCAGCAGA
EST: gi|148980136|gb|EE026970.2|EE026970
EST:     GGTGGTGATGACGACGATGCTATAAACATAATTAAGATGGACAATGAAAG                         GGAGTTTTTGGTTGATCTGATGGCTGCTCCTGGTGCTCTTATTCCAGCAGA
genomic: GGTGGTGATGACGACGATGCTATAAACATAATTAAGATGGACAATGAAAGgtatcaatgt ... ttttctgtagGGAGTTTTTGGTTGATCTGATGGCTGCTCCTGGTGCTCTTATTCCAGCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttgttgctactctatgtttactaagtagttttttggttaaatttttctgtagGGAGTTTTTGGTTGATCTGATGGCTGCTCCTGGTGCTCTTATTCCAGCAGATATCTTAAGTTGGAAAGGCAATTCGTTAAATTCTAATCGAAAACTCGGC
 aattaat  putative branch site (score: 3)
                                            tttttctgt  putative PPT
                            tagttttttggttaaa  TA-rich tract