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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatcgtgtgatttgttttttcaacatgatcagcagtgggttctgtaacacagttatgctgtctatatactacagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGATGGAAAAAGTTACAGTACCAATTTGGCATTTACGCCTCCAGAATACATGA

Basic information

species Zea mays
transcript GRMZM2G382104_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g58750.2 (Oryza sativa), 3'ss of exon 5
gtgagtatcgtgtgatttgttttttcaacatgatcagcagtgggttctgtaacacagttatgctgtctatatactacagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGATGGAAAAAGTTACAGTACCAATTTGGCATTTACGCCTCCAGAATACATGA
||||||||| | |   ||||||||  ||| |||||| | ||| ||| |||||||    |||| ||| || ||   |||||||||||||||||| ||||| ||||| || |||||||||||||| || ||||| ||||| |||||||||||| |||| ||||| |||||||| |||||||
gtgagtatcatatagattgtttttgtaacgtgatcatctgtgtgttttgtaacatttctatgttgtttacatggcacagGACTGTAACCCTAGGCTTTCATGTTTTGGCCTCATGAAGAACAGTCGAGATGGTAAAAGCTACAGTACCAATCTGGCGTTTACTCCTCCAGAGTACATGA

upper sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G07850.2 (Glycine max), 3'ss of exon 5
gtgagtatcgtgtg-atttgttttttcaacatgatcagcagtgggttctgtaacacagttatgctgtctatatactacagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGATGGAAAAAGTTACAGTACCAATTTGGCATTTACGCCTCCAGAATACATGA
|| ||| |  |||| ||    |||||  |||||  |  || |   |    ||| | |   ||| |||    ||  | |||||  |||| ||||| |||||  |||| ||||| ||||| || ||| ||||||| |||||||| || || |||||||||||||| |||||||| ||  | |
gtaagt-ttttgtgtatcccctttttatacatgtcc--caataattagattaata-aaaaatg-tgttagaattttgcagGATGGTAATCCTAGGCTTTCAAGTTTTGGTCTTATGAAAAATAGCAGGGATGGGAAAAGTTATAGCACAAATTTGGCATTTACCCCTCCAGAGTATCTTA

upper sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA03G01300.2 (Glycine max), 3'ss of exon 5
gtgagtatcgtgtg-atttgttttttcaacatgatcagcagtgggttctgtaacacagttatgctgtctatatactacagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGATGGAAAAAGTTACAGTACCAATTTGGCATTTACGCCTCCAGAATACATGA
|| ||| |  |||| ||    |||||  |||||  |  |  |   |    ||| | |   ||| |||    ||  | |||||  |||| ||||| |||||  |||| ||||| ||||| || ||| ||||||| |||||||| || || |||||||||||||| |||||||| ||  | |
gtaagt-ttttgtgtatcccctttttatacatgtcc--ctataattagattaataaaaaaatg-tgttagaattttgcagGATGGTAATCCTAGGCTTTCGAGTTTTGGTCTTATGAAAAATAGCAGGGATGGGAAAAGTTATAGCACAAATTTGGCATTTACCCCTCCAGAGTATCTCA

upper sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA05G37870.1 (Glycine max), 3'ss of exon 6
-----------------gtgagtatcgtgtgatt-tgttttttcaacatgatcagca---gtgggttctgtaacacagttatgctgtctatatactacagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGATGGAAAAAGTTACAGTACCAATTTGGCATTTACGCCTCCAGAATACATGA
                 |  | |    |    ||  || || | | | | |  || |   || |  | |         || | |   |  | |  | |||||||  || ||||||||||| || |||||||| ||||| || ||  ||||||| | |||||||||||| |||||||| ||||| || || |||||  |||
tgggtggagctgtggaagaaactgctataaatttgcgtgttcttagcctaaatagtaagtgttgactgtcctttttcttttttccccccttgttatgcagGACTACAATCCTAGACTTTCATGCTTCGGTCTGATGAAAAATAGTAGGGATGGGAGAAGTTACAGTACAAATTTGGCGTTTACTCCACCTGAATATCTGA

upper sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G01730.2 (Glycine max), 3'ss of exon 5
------------------gtgagtatcgtgtgatt-tgttttttcaacatgatcagcagtgggttctgtaacacagttatgctgtctatatacta--cagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGATGGAAAAAGTTACAGTACCAATTTGGCATTTACGCCTCCAGAATACATGA
                  |  | |    |    |  || ||| | | | | |  || |   |   ||||        | |  |  ||   || ||  ||||| |  || ||||||||||| || |||||||| ||||| || ||  | ||||| |||||||||||||| ||||||||||| || || || |||||  |||
ggcactgatactgtggaagaaactgctataaattagtgctttcttagcctaaatagtatgtgtgactgtcctttttctttttttcctccttattattcagGAATACAATCCTAGACTTTCATGCTTCGGTCTGATGAAAAATAGTAGAGATGGGAAAAGTTACAGTACAAATTTGGCATTCACTCCACCTGAATATCTGA

upper sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S156_133V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------gtgagtatcgtgtgatttgttttttcaacatgatcagcagtgggttctgtaacacagttatg-ctgtctatatacta-cagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGATGGAAAAAGTTACAGTACCAATTTGGCATTTACGCCTCCAGAATACATGA
                       ||    |  || | |||   |   |  | |     ||       | ||    | |||||  | |||  |   || |||||  |  ||||  | || |||||||| || ||||||||||||||| | ||||| ||||| ||||| |||||| |||| |  || ||||| || ||| | |
ttttgtggtttttcctttgaactagctctgcttggtatgtggatgttaactaaagtctagaaaacggt-tagtttatttatggttatctgcaatttatcagGATGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTACTTAA

upper sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S122_66V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------------------------------------------------gtgagtatcgtg-tgatttgttttttc--aacatga---tcagcagtgggt--------tctgta----acacagttatgctgtct---atatactacagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGATGGAAAAAGTTACAGTACCAATTTGGCATTTACGCCTCCAGAATACATGA
                                                                                                    | ||   |  | | || ||||| |  || || |   |    ||| |          ||||||    | | | | ||| | ||       |    |||||  |  | ||  | || || ||||| || |||||||||||||| || ||||||||||| || ||||||||| |||| |  || || || |||||| | |
gtattgctcttctctgtagcagttttgaactaaaacttggtatgtcccttcccgttcctatcaagtctcgacaatcctgctatacagaacacccacatcaaatacgctaatcacttttttttacggaaaataaggttttaaagtagacctatctaatctgtagattataaattgatggtctcccacgcctttgtcagGAAGGAGATCCGCGCCTCTCTTGTTTTGGCCTCATGAAGAACAGTCGCGATGGAAAAAGCTATAGTACCAATCTGGCCTACACTCCCCCTGAATACTTAA

upper sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S9_348V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------gtgagtatcgtgtgatttgttt-tttcaac-atgatcagcagtgggttctgtaacacagttatgctgtctatatactacagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGATGGAAAAAGTTACAGTACCAATTTGGCATTTACGCCTCCAGAATACATGA
                       |||      |  |  ||   |||||||     | |  ||   | || |||    |   || || |    ||  |  ||||| |  ||||  | || |||||||| || ||||||||||||||| | ||||||||||| ||||| ||||||||||| |  || ||||| || ||| |||
tcgtgtgggtttcctttggaaatagttctacttagtacgtggatttcaactgcagttaatagaatgctcagtatattaacgattctctacg-attttgtagGACGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGAAAAAGCTACAGCACCAATTTGGCTTACACTCCTCCTGAGTACTTGA

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|211173516|gb|FK981111.1|FK981111
EST:     GCCGTGCTCTCTACCATGATCTCAATGCCTATAGAGCTCTGTTTGATGAT                         GACTGTAACCCTAGACTTTCCTGTTTCGGCCTCATGAAGAACAGTCGGGAT
genomic: GCCGTGCTCTCTACCATGATCTCAATGCCTATAGAGCTCTGTTTGATGATgtgagtatcg ... tatactacagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGAT
EST: gi|211173514|gb|FK981109.1|FK981109
EST:     GCCGTGCTCTCTACCATGATCTCAATGCCTATAGAGCTCTGTTTGATGAT                         GACTGTAACCCTAGACTTTCCTGTTTCGGCCTCATGAAGAACAGTCGGGAT
genomic: GCCGTGCTCTCTACCATGATCTCAATGCCTATAGAGCTCTGTTTGATGATgtgagtatcg ... tatactacagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaacatgatcagcagtgggttctgtaacacagttatgctgtctatatactacagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGATGGAAAAAGTTACAGTACCAATTTGGCATTTACGCCTCCAGAATACATGA
                      ctgtaac  putative branch site (score: 3)
                                           tatatacta  TA-rich tract