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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgtgtaacataattgcatcacactccctgacatttgctgttatattaaccatttacttttttccaattgaagTTTACCTGTTGTCCAAGGATTAGCCACTGAAGTCAAGAAGACAGTGCAATCATTAGTTTCACAGCTTCTCCAGAAACTTCGATCAAATATTCAG

Basic information

species Zea mays
transcript GRMZM2G006781_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006781_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g35290.1 (Oryza sativa), 3'ss of exon 4
gtatgttgtgtaacataat-tgcatcacactccctgacatttgctgttatattaaccatttacttttttccaattgaagTTTACCTGTTGTCCAAGGATTAGCCACTGAAGTCAAGAAGACAGTGCAATCATTAGTTTCACAGCTTCTCCAGAAACTTCGATCAAATATTCAG
||| ||  | | ||||||| |  || |    |  ||  ||||||  |||  |||||  | | | ||||  | ||||||||||||||||| ||||||| |||||   |||||||||||||||| | || |||||| |||| |||||||||||||| ||||||||||||||||||
gtaagtcatttgacataatctttattatggcctttgtaatttgcaattaatttaactgtatgcctttt--cgattgaagTTTACCTGTTATCCAAGGCTTAGCTGTTGAAGTCAAGAAGACAATACAGTCATTAATTTCTCAGCTTCTCCAGAAGCTTCGATCAAATATTCAG

upper sequence: GRMZM2G006781_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA16G22880.1 (Glycine max), 3'ss of exon 3
-------------------------------------gtatgttgtgtaacataattgcatcacactccctgacatt---------tgctgttatatta--accatttacttttttccaattga-agTTTACCTGTTGTCCAAGGATTAGCCACTGAAGTCAAGAAGACAGTGCAATCATTAGTTTCACAGCTTCTCCAGAAACTTCGATCAAATATTCAG
                                      |||  | |  || | ||||   |  |   |  | | |||         |  | |||| ||   || |  |  ||||  |   |  | || ||||| ||| | ||||  || ||  | ||||| | |  |||    |||||| |  |||| |||||||| ||||||||||| ||||||||||||
gtaagtttatatgcttcttccatgctgtttacaattaatatacttttaaatagaattctttttcttccatttatattatattattttatttttatgttgttactaaatgtttttcccgggtgcatagGTTACCAGTTATTCAAGCGTTGGCTGCAGAAGTTAGGCTGACTACCCAATCACTTCTTTCTCAGCTTCTACAGAAACTTCGCTCAAATATTCAG

upper sequence: GRMZM2G006781_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G04920.1 (Glycine max), 3'ss of exon 3
----------------------------------------------------gtatgttgtgtaacataattgcatcacactccctgacatttgctgttatattaaccatttacttttttccaat-tgaagTTTACCTGTTGTCCAAGGATTAGCCACTGAAGTCAAGAAGACAGTGCAATCATTAGTTTCACAGCTTCTCCAGAAACTTCGATCAAATATTCAG
                                                    | ||  | | |     | ||  || | | |   | |  |||    |  | |||   |  |  |||| |    |   ||| ||||| ||| | ||||  || ||  | || || | |  |||    |||||| |  |||| |||||||| ||||||||||| ||||||||||||
gtaagtttatatgcttcttccatgctgtttacaattaatatacctttaaataggattctttttcttccagttttataatattattttatttttctgttcttgttactaaaatgtttttcttgggtgcaaagGTTACCAGTTATTCAAGCGTTGGCTGCAGATGTTAGGCTGACTACCCAATCACTTCTTTCTCAGCTTCTTCAGAAACTTCGCTCAAATATTCAG

upper sequence: GRMZM2G006781_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv04s0008g01350.t01 (Vitis vinifera), 3'ss of exon 4
-----------------gtatgttgtgtaaca--taat-tgcatcacactccctgacatttgctgttata-ttaaccatttactt--ttttccaattgaagTTTACCTGTTGTCCAAGGATTAGCCACTGAAGTCAAGAAGACAGTGCAATCATTAGTTTCACAGCTTCTCCAGAAACTTCGATCAAATATTCAG
                 ||||| |   |  ||  |||| |   |   |       || ||      | ||  | || |||  | |  |||| |  || ||| || || ||  | |||| | | ||  | ||||| | | | |||   |||||  |  ||   ||||||||||||||||||||||||||||||| |
gtgagcttttatttcttgtatgctacttgccaactaatatttgttttagctgtcaaccttgagaaatgtaactcactattgccctgttttttcgcttaaagATTGCCAGTCATTCAAGCACTGGCTGCAGAAGTTAGGCAAACAACCCAATCTCTTCTTCATCAGCTTCTCCAGAAACTTCGATCAAATATTCTG

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|149008084|gb|EE040323.2|EE040323
EST:     GCACTTGACCTAGAAGCTTTTGTGAGCAAAATCTGGAAGTTGCACCCTGA                         TTTACCTGTTGTCCAAGGATTAGCCACTGAAGTCAAGAAGACAGTGCAATC
genomic: GCACTTGACCTAGAAGCTTTTGTGAGCAAAATCTGGAAGTTGCACCCTGAgtatgttgtg ... ccaattgaagTTTACCTGTTGTCCAAGGATTAGCCACTGAAGTCAAGAAGACAGTGCAATC
EST: gi|148939698|gb|EC884368.2|EC884368
EST:     GCACTTGACCTAGAAGCTTTTGTGAGCAAAATCTGGAAGTTGCACCCTGA                         TTTACCTGTTGTCCAAGGATTAGCCACTGAAGTCAAGAAGACAGTGCAATC
genomic: GCACTTGACCTAGAAGCTTTTGTGAGCAAAATCTGGAAGTTGCACCCTGAgtatgttgtg ... ccaattgaagTTTACCTGTTGTCCAAGGATTAGCCACTGAAGTCAAGAAGACAGTGCAATC
EST: gi|148963434|gb|EE014450.2|EE014450
EST:     GCACTTGACCTAGAAGCTTTTGTGAGCAAAATCTGGAAGTTGCACCCTGA                         TTTACCTGTTGTCCAAGGATTAGCCACTGAAGTCAAGAAGACAGTGCAATC
genomic: GCACTTGACCTAGAAGCTTTTGTGAGCAAAATCTGGAAGTTGCACCCTGAgtatgttgtg ... ccaattgaagTTTACCTGTTGTCCAAGGATTAGCCACTGAAGTCAAGAAGACAGTGCAATC
EST: gi|4730483|gb|AI649649.1|AI649649
EST:     GCACTTGACCTAGAAGCTTTTGTGAGCAAAATCTGGAAGTTGCACCCTGA                         TTTACCTGTTGTCCAAGGATT
genomic: GCACTTGACCTAGAAGCTTTTGTGAGCAAAATCTGGAAGTTGCACCCTGAgtatgttgtg ... ccaattgaagTTTACCTGTTGTCCAAGGATT
EST: gi|211334830|gb|FL416303.1|FL416303
EST:     ACTTGACCTAGAAGCTTTTGTGAAGCAAAATCTGGAAAGTTGCACCCTGA                         TTTAACCTGTTGGTCCAAGGGAT-AGCCCCCTGAAGTC
genomic: ACTTGACCTAGAAGCTTTTGTGA-GCAAAATCTGGAA-GTTGCACCCTGAgtatgttgtg ... ccaattgaagTTTA-CCTGTTG-TCCAAGG-ATTAGCCAC-TGAAGTC
EST: gi|71305530|gb|DR788908.1|DR788908
EST:     GCACTTGACCTAGAAGCTTTTGTGAGCAAAATCTGGAAGTTGCACCCTGA                         TTTACCTGTTGTCCAAGGATTAGCCACTGAAGTCAAGAAGACAGTGCAATC
genomic: GCACTTGACCTAGAAGCTTTTGTGAGCAAAATCTGGAAGTTGCACCCTGAgtatgttgtg ... ccaattgaagTTTACCTGTTGTCCAAGGATTAGCCACTGAAGTCAAGAAGACAGTGCAATC
EST: gi|86469576|gb|DY235946.1|DY235946
EST:     GCACTTGACCTAAAAGCTTTTGTGAGCAAAATCTGGAAGTTGCACCCTGA                         TTTACCTGTTGTCCAAGGATTACCCACTGAAGTCAAGAAGACAGTGCACTC
genomic: GCACTTGACCTAGAAGCTTTTGTGAGCAAAATCTGGAAGTTGCACCCTGAgtatgttgtg ... ccaattgaagTTTACCTGTTGTCCAAGGATTAGCCACTGAAGTCAAGAAGACAGTGCAATC
EST: gi|211082178|gb|FL396889.1|FL396889
EST:     CACTTGACCTAGAAGCTTTTGTGAGCAAAAATCTGGAAGTTGCACCCTGA                         TTTACCTGTTGTCCAAGGATTAGCCACTGAAGTCAAGGAGACAGTGCAATC
genomic: CACTTGACCTAGAAGCTTTTGTGAGCAAAA-TCTGGAAGTTGCACCCTGAgtatgttgtg ... ccaattgaagTTTACCTGTTGTCCAAGGATTAGCCACTGAAGTCAAGAAGACAGTGCAATC
EST: gi|71449856|gb|DR830906.1|DR830906
EST:     GCACTTGACCTAGAAGCTTTTGTGAGCAAAATCTGGAAGTTGCACCCTGA                         TTTACCTGTTGTCCAAGGATTAGCCACTGAAGTCAAGAAGACAGTGCAATC
genomic: GCACTTGACCTAGAAGCTTTTGTGAGCAAAATCTGGAAGTTGCACCCTGAgtatgttgtg ... ccaattgaagTTTACCTGTTGTCCAAGGATTAGCCACTGAAGTCAAGAAGACAGTGCAATC
EST: gi|148999331|gb|EE036267.2|EE036267
EST:     GCACTTGACCTAGAAGCTTTTGTGAGCAAAATCTGGAAGTTGCACCCTGA                         TTTACCTGTTGTCCAAGGATTAGCCACTGAAGTCAAGAAGACAGTGCAATC
genomic: GCACTTGACCTAGAAGCTTTTGTGAGCAAAATCTGGAAGTTGCACCCTGAgtatgttgtg ... ccaattgaagTTTACCTGTTGTCCAAGGATTAGCCACTGAAGTCAAGAAGACAGTGCAATC
EST: gi|148979834|gb|EE026851.2|EE026851
EST:     GCACTTGACCTAGAAGCTTTTGTGAGCAAAATCTGGAAGTTGCACCCTGA                         TTTACCTGTTGTCCAAGGATTAGCCACTGAAGTCAAGAAGACAGTGCAATC
genomic: GCACTTGACCTAGAAGCTTTTGTGAGCAAAATCTGGAAGTTGCACCCTGAgtatgttgtg ... ccaattgaagTTTACCTGTTGTCCAAGGATTAGCCACTGAAGTCAAGAAGACAGTGCAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacactccctgacatttgctgttatattaaccatttacttttttccaattgaagTTTACCTGTTGTCCAAGGATTAGCCACTGAAGTCAAGAAGACAGTGCAATCATTAGTTTCACAGCTTCTCCAGAAACTTCGATCAAATATTCAG
                         tattaac  putative branch site (score: 1)
                               ccatttacttttttcc  CT-rich tract
                      ttatattaaccattta  TA-rich tract