Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttaacatcccattaaaattctctcccattccatcagattttacagtaatcctagaatgattattcagtagtgtattctgattttttggactttgtagGTGTTGACATCAGCATGAATACTCATCTGAAGACTGTGAAGCTGACACTAAAAGGGAAAAATCCTGTTACCCTTGATCACCTTAGTGTGAGGGGAAACAA

Basic information

species Zea mays
transcript GRMZM2G416061_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G416061_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g37430.1 (Oryza sativa), 3'ss of exon 2
tttttaacatcccattaaaattctctcccattccatcagattttacagtaatcctagaatgattattcagtagtgtattctgattttttgg---actttgtagGTGTTGACATCAGCATGAATACTCATCTGAAGACTGTGAAGCTGACACTAAAAGGGAAAAATCCTGTTACCCTTGATCACCTTAGTGTGAGGGGAAACAA
|    |         | |     ||   | |   ||||  |     ||| |  | |   | ||  | ||   |   || || | ||   ||   | |||||||||||||| ||||||||||| || || ||||| |||||||| || ||| | ||||||||||||||||||||| |||||||||| |||||||||||||||||
tcagcagagctattctcatgcggtcatgcctataatcacctccataagtgactcca---ttatactccatatgcacatcctaacttccaggtctattttgtagGTGTTGATATCAGCATGAACACGCACCTGAAAACTGTGAAACTCACATTGAAAGGGAAAAATCCTGTTACCTTTGATCACCTCAGTGTGAGGGGAAACAA

upper sequence: GRMZM2G416061_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G52210.1 (Glycine max), 3'ss of exon 3
tttttaacatcccattaaaattctctcccattcca-tcagattttac-agtaatcctagaatgattattcagtagtgtattctgattttttggactttgt---agGTGTTGACATCAGCATGAATACTCATCTGAAGACTGTGAAGCTGACACTAAAAGGGAAAAATCCTGTTACCCTTGATCACCTTAGTGTGAGGGGAAACAA-
    | |  |||  |||  ||  |    | | | | |   | |  || |  ||   ||  |     | ||  |||  ||  |||||| |  |   ||||    ||||||||| ||||| ||||| || ||| |||| || || || || || || |||||||||||||| || || || ||||| || ||||||||||| ||||| 
--agtga-gtcctcttactatattgctgcttcctagttgaactacaccaacaactttaagacaggaagtct-tagctta--ctgattctgggatttttgccacaggTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAATCCAGTGACTCTGGATCATCTCAGTGTGAGGGGTAACAAC

upper sequence: GRMZM2G416061_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G10640.1 (Glycine max), 3'ss of exon 3
tttttaacatcccattaaaattctctcccattcca-tcagattttac-agtaatcctagaatgattattcagtagtgtattctgattttttggactttgt---agGTGTTGACATCAGCATGAATACTCATCTGAAGACTGTGAAGCTGACACTAAAAGGGAAAAATCCTGTTACCCTTGATCACCTTAGTGTGAGGGGAAACAA
|  | |   |||  |||  ||  |    | ||| | |   | |  || || ||   ||  |     | ||  |||  ||  |||||| |  |   ||||    ||||||||| ||||| ||||| || ||| |||| || || || || || || |||||||||||||| || || || ||||| || ||||||||||| |||||
tagtcag--tccttttactatcttgcttctttctagttgaactacaccagcaactttaagagaggaagtct-tagctta--ctgattctgggacttttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAATCCAGTCACTCTAGATCATCTCAGTGTGAGGGGTAACAA

upper sequence: GRMZM2G416061_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv19s0015g01330.t01 (Vitis vinifera), 3'ss of exon 2
tttttaacatcccattaa-aattctctcccattccatcagat-tttacagtaatcctagaatgattattcagtagtgtattctgattttttggactttgtagGTGTTGACATCAGCATGAATACTCATCTGAAGACTGTGAAGCTGACACTAAAAGGGAAAAATCCTGTTACCCTTGATCACCTTAGTGTGAGGGGAAACAA
    |||| |    |    || ||  |   ||  ||  |  | |||| | | |     || ||   |     | |   ||  |  |  |||| |  || ||||||| || || || ||||| || ||| ||||||||||||| ||||| || || ||||||||||| || ||  | |||||||| ||||||||||| |||||
--agtaacttgaagtaggtaagtccatgttatgacaaaaactatttagaatcaaagatgattggagagatcattgctgatggtattgctttgtatgttatagGTGTGGATATTAGTATGAACACACATTTGAAGACTGTGAAACTGACTCTGAAGGGGAAAAATCCAGTGACTATGGATCACCTGAGTGTGAGGGGCAACAA

upper sequence: GRMZM2G416061_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S726_1V6.1 (Physcomitrella patens), 3'ss of exon 2
tttttaacatcccattaaaattctctcccattccatcagattttacagt-aatcctagaatgattattcagtagtgtattctgattttttgga-----ctttgtagGTGTTGACATCAGCATGAATACTCATCTGAAGACTGTGAAGCTGACACTAAAAGGGAAAAATCCTGTTACCCTTGATCACCTTAGTGTGAGGGGAAACAA
||| |   || ||||  |  ||  | |  | | | ||| ||    | || || |      ||| ||||    |||   |  |||||  |||        |||| |||||| || ||||||||||| || ||| ||||| ||||||||||||| || || || ||   ||| ||  | || || ||||| ||| |  | || || ||
tttgttttattccat--agcttaacccttagttcttca-atagcgcggttaaacgctagttgaatatttcacagt---tgttgattgcttgagagctcttttgcagGTGTGGATATCAGCATGAACACCCATTTGAAGTCTGTGAAGCTGACTCTGAAGGGCAAGGTTCCCGTGTCTCTCGACCACCTCAGTATCCGTGGCAATAA

upper sequence: GRMZM2G416061_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S37_118V6.1 (Physcomitrella patens), 3'ss of exon 2
--tttttaacatcccattaaaattctctcccattccatcagattttacagtaatcctagaatgattattcagtagtgtattctgattttttggactttgtagGTGTTGACATCAGCATGAATACTCATCTGAAGACTGTGAAGCTGACACTAAAAGGGAAAAATCCTGTTACCCTTGATCACCTTAGTGTGAGGGGAAACAA
    ||    |    |  |||| |         |  |  | |  |  |  |    | | || |||     ||| || |  | | |||  || |  || | |||||| || |||||||||||||| ||| ||||| |||||||||| ||  | || || ||   ||||||  | || || || || |||||  | || |||||
cagcttggctactgtacgaaaaatgcggaattctgtaataaacatagctttctggcgaaaacgatggcg-agtcgt-tgatgttattacttcgttttcgcagGTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGAAGGGAAAGGTTCCTGTGGCTCTCGACCATCTCAGTGTCCGCGGCAACAA

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|211058973|gb|FL460147.1|FL460147
EST:     GTTATCCGGTCGATTATGGTTTACATATACGGACAGCTATCTTCAGATA                         GTGTTGACATCAGCATGAATACTCATCTGAAGACTGTGAAGCTGACACTAA
genomic: GTTATCCGGTCGATTATGGTTTACATATACGGACAGCTATCTTCAGATAgttaagtaat ... gactttgtagGTGTTGACATCAGCATGAATACTCATCTGAAGACTGTGAAGCTGACACTAA
EST: gi|60353877|gb|DN220850.1|DN220850
EST:     GTTATCCGGTCGATTATGGTTTACATATACGGACAGCTATCTTCAGATA                         GTGTTGACATCAGCATGAATACTCATCTGAAGACTGTGAAGCTGACACTAA
genomic: GTTATCCGGTCGATTATGGTTTACATATACGGACAGCTATCTTCAGATAgttaagtaat ... gactttgtagGTGTTGACATCAGCATGAATACTCATCTGAAGACTGTGAAGCTGACACTAA
EST: gi|211405279|gb|FL027503.1|FL027503
EST:     GTTATCCGGTCGATTATGGTTTACATATACGGACAGCTATCTTCAGATA                         GCGTTGACATCAGCATGAATACTCATCTGAAGACTGTGAAGCTGACACTAA
genomic: GTTATCCGGTCGATTATGGTTTACATATACGGACAGCTATCTTCAGATAgttaagtaat ... gactttgtagGTGTTGACATCAGCATGAATACTCATCTGAAGACTGTGAAGCTGACACTAA
EST: gi|211405278|gb|FL027502.1|FL027502
EST:     GTTATCCGGTCGATTATGGTTTACATATACGGACAGCTATCTTCAGATA                         GTGTTGACATCAGCATGAATACTCATCTGAAGACTGTGAAGCTGACACTAA
genomic: GTTATCCGGTCGATTATGGTTTACATATACGGACAGCTATCTTCAGATAgttaagtaat ... gactttgtagGTGTTGACATCAGCATGAATACTCATCTGAAGACTGTGAAGCTGACACTAA
EST: gi|211405280|gb|FL027504.1|FL027504
EST:     GTTATCCGGTCGATTATGGTTTACATATACGGACAGCTATCTTCAGATA                         GTGTTGACATCAGCATGAATACTCATCTGAAGACTGTGAAGCTGACACTAA
genomic: GTTATCCGGTCGATTATGGTTTACATATACGGACAGCTATCTTCAGATAgttaagtaat ... gactttgtagGTGTTGACATCAGCATGAATACTCATCTGAAGACTGTGAAGCTGACACTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtaatcctagaatgattattcagtagtgtattctgattttttggactttgtagGTGTTGACATCAGCATGAATACTCATCTGAAGACTGTGAAGCTGACACTAAAAGGGAAAAATCCTGTTACCCTTGATCACCTTAGTGTGAGGGGAAACAA
                                ttctgat  putative branch site (score: 3)
                              tattctgatttttt  TA-rich tract