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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcattcttaaagagatgttgcttcaattattgtcaccatgattctttttcaccttgtcttaattccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGTTTGAGAGTGGCAGAGTATGCTTTCCATTATGCCAAGGCCAATGGCCGGG

Basic information

species Zea mays
transcript GRMZM2G120857_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120857_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 4
gtaagcattcttaaa-gagatgttgcttcaattattgtcaccatgattctttttcaccttgtcttaattccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGTTTGAGAGTGGCAGAGTATGCTTTCCATTATGCCAAGGCCAATGGCCGGG
||||||||||||||| |  || |   ||  |||  | |    |  ||| ||  ||||  |||  || ||   || ||||||||||| |||||||||||||| || |||||||| || |||||||||||||| ||||||||||||||||||||||| ||||||||| ||||||||||||
gtaagcattcttaaaagcaatatcattttcattggtcttgttagcattattcatcactgtgtgctatttattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGTTTAAGAGTGGCAGAGTATGCTTTCCACTATGCCAAGACCAATGGCCGGG

upper sequence: GRMZM2G120857_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G06590.2 (Glycine max), 3'ss of exon 2
gtaagcattctta-aagagatgttgctt-caattattgtcaccatgat---tctttttcaccttgtcttaattccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGTTTGAGAGTGGCAGAGTATGCTTTCCATTATGCCAAGGCCAATGGCCGGG
||||   |    | ||  |||||| | | | || ||| | |   ||||   | |  ||    | |  || ||      ||||||||||||||||||||| |||||| | ||||| |||||||| ||||||||||| || || || ||||||||||| || |||||||||||  ||||  | |
gtaaatttcacaacaattgatgttacatactatcattttaattctgatcaatataatttgtttagcatttatgg-gtctcagGTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGTTTAAGGGTAGCTGAGTATGCTTTTCACTATGCCAAGGCTCATGGAAGAG

upper sequence: GRMZM2G120857_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G20790.1 (Glycine max), 3'ss of exon 2
gtaagcattcttaaagagatgttgcttcaattattgtc---accatgattctttt--tcaccttgtcttaattccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGTTTGAGAGTGGCAGAGTATGCTTTCCATTATGCCAAGGCCAATGGCCGGG
||||  |||    || |  |  |||    | |||  ||   |   ||||   | |  |    ||  | |  ||    ||||||||||||||||||| || |||||| | ||||| |||||||| ||||||||||| || || || ||||||||||| || |||||||||||  ||||  | |
gtaa--atttcacaacaatttatgcacgtactatcatctgaattctgatcaatataatttgtttagcatttttgggtttcagGTTGTGAGAGGTGTAGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGTTTAAGGGTAGCTGAGTATGCTTTTCACTATGCCAAGGCTCATGGAAGAG

upper sequence: GRMZM2G120857_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT5G03290.1 (Arabidopsis thaliana), 3'ss of exon 2
------------gtaagcattcttaaagag-atgttgcttcaattattgtcacca-tgattctt-------tttcaccttgtcttaattc-cacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGTTTGAGAGTGGCAGAGTATGCTTTCCATTATGCCAAGGCCAATGGCCGGG
             ||||  |  | |  ||  || |    | | || || | |  | |||||||        |||    || || | |  |  |    ||||||| |||||||| ||||||||| | ||||| ||||| || || || ||||||||||| |||||||||||||| |  ||||||||| |  ||||  | |
gtttagtttgttttaagtctattgatcgaatatttcaggttagttcttctaataaatgattctaatgatggttttgttttctcctgacgcatataatagGTTGTTAGAGGTGTGGTGGAAAGTCTTAAAATCATTACCCGTCAGGCGAGTTTGAGAGTTGCAGAGTATGCTTTTCTCTATGCCAAGACTCATGGAAGAG

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|32927267|gb|CF032079.1|CF032079
EST:     TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT
genomic: TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... tccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT
EST: gi|32929253|gb|CF034065.1|CF034065
EST:     TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT
genomic: TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... tccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT
EST: gi|23199568|gb|BU582133.1|BU582133
EST:     T-ACAATTCG-GAAAATACTGAAGGAGAATATAG-GGTCTTGAGCATCAG                         GTTGTGAGAGG-GTTG-GGAAAGTTTGAAAATTATTACACGCCAAGCAAGT
genomic: TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... tccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT
EST: gi|87155757|gb|DY400546.1|DY400546
EST:     TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT
genomic: TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... tccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT
EST: gi|110201588|gb|EC883485.1|EC883485
EST:     TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTGGAAAGTTTGAAAAATTATTACACGCCAAGCAAG
genomic: TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... tccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAA-TTATTACACGCCAAGCAAG
EST: gi|71429827|gb|DR810877.1|DR810877
EST:     TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTGGAAAGTTTGAAAAATATTACACGCCCAAGCA-G
genomic: TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... tccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCC-AAGCAAG
EST: gi|78109386|gb|DV527802.1|DV527802
EST:     TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT
genomic: TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... tccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT
EST: gi|9731686|gb|BE510438.1|BE510438
EST:     TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT
genomic: TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... tccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT
EST: gi|40335589|gb|CK369659.1|CK369659
EST:     TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT
genomic: TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... tccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT
EST: gi|32931400|gb|CF036212.1|CF036212
EST:     TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAG                         GTTGTGAGAGGTGTTGTGGAAAGTTTAAAAATTATTACACGCCAAGCAAGT
genomic: TAACAATTCGTGAAAATACTGAAGGAGAATATAGTGGTCTTGAGCATCAGgtaagcattc ... tccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttcaattattgtcaccatgattctttttcaccttgtcttaattccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGTTTGAGAGTGGCAGAGTATGCTTTCCATTATGCCAAGGCCAATGGCCGGG
                                      tcttaat  putative branch site (score: 3)
                                            ttccacttc  CT-rich tract
      aattattgt  TA-rich tract