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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgaagtatacctatgtgattgtactattgctccatcaatccttcatctttgtccgttttgatgctagcatgaaagactgaaaataactaccatttctaaatgtctgttgggtgcacagattgggatatgacaaatgttgtgattttcagGCCAAGACCACCAAGAAAATCGTATTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAGGTGCAGTGTCTCATTTTCCTGTGTT

Basic information

species Zea mays
transcript GRMZM2G009412_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009412_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g33880.1 (Oryza sativa), 3'ss of exon 2
---------------------------------------gtaatgaagtatacctatgtgattgtactattgctccatcaatccttcatctttgtccgttt---tgatgctagcatgaaagactgaaaataactaccatttctaaatgtctgttgg--gtgcacagattgggatatgacaaatg-ttgtgattttcagGCCAAGACCACCAAGAAAATCGTATTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAGGTGCAGTGTCTCATTTTCCTGTGTT
                                       || |     | | | | |   |  ||||  |  |   ||  ||    ||    | |  || |     ||||  |    ||  ||    |   | |   | ||  |  || || |  |  |||||    |   | ||||| | ||| ||    ||||||||| || ||||||||||| |||||  |||||||||| ||||| ||||||||||| ||||| |||||| | || |||                         
gtactgtgacagtttatatatgattatgcagtgttgtgtgtgactctctgttcat-tagaaacgtacggtgtcatgattgatgtagcagtgatatgtgtctgtacaatgcatgtggcaataaccatcacgtagttttaattgcatgtggctttcagctgtgcatttttcatgttatgatacatggttcctgttttcagGCAAAAACCACCAAGAAGATCGTGCTGAAGCTGCAATGCCAAAGCTGCAAGCATTACTCCCAGCACCCCATCAAG-------------------------

upper sequence: GRMZM2G009412_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g33915.1 (Oryza sativa), 3'ss of exon 1
gtaatgaagtatacctatgtgattgtactattgctccatcaatccttcatctttgtccgttttgatgctagcatgaaagactgaaaataactaccatttctaaatgtctgttgggtgcacagattgggatatgacaaatg-ttgtgattttcagGCCAAGACCACCAAGAAAATCGTATTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAGGTGCAGTGTCTCATTTTCCTGTGTT
                                                        || |   |   |  ||       | ||    |  |  ||              |  |||||||    |   | ||||| | ||| ||    ||||||||| || ||||||||||| || ||  |||||||||| ||||| ||||||||||| ||||| |||||| | || |||                         
-----------------------------------------------------gccccatcgcgccacc-gcgcacggcattgttgctctcctccggccaggtccaaaagcagggtgcatttttcatgttatgatacatggttcctgttttcagGCAAAAACCACCAAGAAGATTGTGCTGAAGCTGCAATGCCAAAGCTGCAAGCATTACTCCCAGCACCCCATCAAG-------------------------

upper sequence: GRMZM2G009412_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g33860.1 (Oryza sativa), 3'ss of exon 2
gtaatgaagtatacctatgtgattgtactattgctccatcaatccttcatctttgtccgttttgatgctagcatgaaagactgaaaataactaccattt---ctaaatgtctgttgg--gtgcacagattgggatatgacaaatg-ttgtgattttcagGCCAAGACCACCAAGAAAATCGTATTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAGGTGCAGTGTCTCATTTTCCTGTGTT
                                                            ||  |||| | ||||    | | |  || ||     |||    || ||| || |  |  |||||    |   | ||||| | ||| ||    ||||||||| || ||||||||||| || ||  |||||||||| ||||| ||||||||||| ||||| |||||| | || |||                         
-----------------------------------------------------------gttcaatgcaaacatgtggtaataaccatcacgtagttttaaagtatatgactttcagctgtgcatttttcatgttatgatacatggttcctgttttcagGCAAAAACCACCAAGAAGATTGTGCTGAAGCTGCAATGCCAAAGCTGCAAGCATTACTCCCAGCACCCCATCAAG-------------------------

upper sequence: GRMZM2G009412_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g33898.1 (Oryza sativa), 3'ss of exon 2
-------------------gtaatgaagta-tacc-tatgtgattgtactattgctccatcaat--------ccttcatctttgtccgttttgatgctagcatgaaagactgaaaataactaccatttctaaatgtctg----ttgg--gtgcacagattgggatatgacaaatg-ttgtgattttcagGCCAAGACCACCAAGAAAATCGTATTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAGGTGCAGTGTCTCATTTTCCTGTGTT
                   || || | | | | |  | |||||||||     | |   |  ||          | | || | |||| |||   |||| | ||||    | | |  || | |    |||  |  | ||||    |  |  |||||    |   | ||||| | ||| ||    ||||||||| || ||||||||||| || ||  |||||||||| ||||| ||||||||||| ||||| |||||| | || |||                         
gtattgtgacagtttatatgtgattacgcagtgctgtgtgtgattgtctctcttcattagaaacatatggtgtcatgatttgtgtctgttc-aatgcaaacatgtggcaataaccatca-tgtagttttaatgtatctgactttcagctgtgcatttttcatgttatgatacatggttcctgttttcagGCAAAAACCACCAAGAAGATTGTGCTGAAGCTGCAATGCCAAAGCTGCAAGCATTACTCCCAGCACCCCATCAAG-------------------------

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|4646348|gb|AI621678.1|AI621678
EST:     GCAAGCAGTCAGGATATGGTGGCCAGACCAAGCCTGTCTTCCACAAGAAG                         GCCAAGACCACCAAGAAAATCGTATTGAAGCTGCAGTGC
genomic: GCAAGCAGTCAGGATATGGTGGCCAGACCAAGCCTGTCTTCCACAAGAAGgtaatgaagt ... tgattttcagGCCAAGACCACCAAGAAAATCGTATTGAAGCTGCAGTGC
EST: gi|211413907|gb|FK968114.1|FK968114
EST:     GCAAGCAGTCAGGATATGGTGGCCAGACCAAGCCTGTCTTCCACAAGAAG                         GCCAAGACCACCAAGAAAATCGTGTTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGCCAGACCAAGCCTGTCTTCCACAAGAAGgtaatgaagt ... tgattttcagGCCAAGACCACCAAGAAAATCGTATTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|32913975|gb|CF018787.1|CF018787
EST:     GCAAGCAGTCAGGATATGGTGGCCAGACCAAGCCTGTCTTCCACAAGAAG                         GCCAAGACCACCAAGAAAATCGTGTTGAAGCTGCAGTGCCAGAGC
genomic: GCAAGCAGTCAGGATATGGTGGCCAGACCAAGCCTGTCTTCCACAAGAAGgtaatgaagt ... tgattttcagGCCAAGACCACCAAGAAAATCGTATTGAAGCTGCAGTGCCAGAGC
EST: gi|116826622|gb|EC870429.1|EC870429
EST:     GCAAGCAGTCAGGATATGGTGGCCAGACCAAGCCTGTCTTCCACAAGAAG                         GCCAAGACCACCAAGAAAATCGTATTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGCCAGACCAAGCCTGTCTTCCACAAGAAGgtaatgaagt ... tgattttcagGCCAAGACCACCAAGAAAATCGTATTGAAGCTGCAGTGCCAGAGCTGCAAG
EST: gi|211511551|gb|FL285070.1|FL285070
EST:     GCAAGCAGTCAGGATATGGTGGCCAGACCAAGCCTGTCTTCCACAAGAAG                         GCCAAGACCACCAAGAAAATCGTGTTGAAGCTGCAGTGCCATGAGCTGCAA
genomic: GCAAGCAGTCAGGATATGGTGGCCAGACCAAGCCTGTCTTCCACAAGAAGgtaatgaagt ... tgattttcagGCCAAGACCACCAAGAAAATCGTATTGAAGCTGCAGTGCCA-GAGCTGCAA
EST: gi|32863442|gb|CF003124.1|CF003124
EST:     GCAAGCAGTCAGGATATGGTGGCCAGACCAAGCCTGTCTTCCACAAGAAG                         GCCAAGACCACCAAG
genomic: GCAAGCAGTCAGGATATGGTGGCCAGACCAAGCCTGTCTTCCACAAGAAGgtaatgaagt ... tgattttcagGCCAAGACCACCAAG
EST: gi|166506113|gb|EG044282.1|EG044282
EST:     GCAAGCAGTCAGGATATGGTGGTCAGACCAAGCCTGTCTTCCACAAGAAG                         GCCAAGACCACCAAGAA
genomic: GCAAGCAGTCAGGATATGGTGGCCAGACCAAGCCTGTCTTCCACAAGAAGgtaatgaagt ... tgattttcagGCCAAGACCACCAAGAA
EST: gi|116822004|gb|EC865370.1|EC865370
EST:     GCAAGCAGTCAGGATATGGTGGCCAGACCAAGCCTGTCTTCCACAAGAAG                         GCCAAGACCACCAAGAAAATCGTATTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGATATGGTGGCCAGACCAAGCCTGTCTTCCACAAGAAGgtaatgaagt ... tgattttcagGCCAAGACCACCAAGAAAATCGTATTGAAGCTGCAGTGCCAGAGCTGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaaatgtctgttgggtgcacagattgggatatgacaaatgttgtgattttcagGCCAAGACCACCAAGAAAATCGTATTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCAATTAAGGTGCAGTGTCTCATTTTCCTGTGTT
 ttctaaa  putative branch site (score: 2)
                                                ttttc  putative PPT
                                     aaatgtt  TA-rich tract