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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactcagcacattcagcgtgtgtgtgtgtgtgcgtgcttgctcgcttaattacctgctgacaacctacgcgcattcaattctcatcagGTGCCAATCGACTGCTTCGAGGAGCAGTGGGTGATCTTCCGAGGCAAAGACGGAAGGCCCGGGTGTGTTCAGAACACATGCGCCCACAGGGCATGCCCGC

Basic information

species Zea mays
transcript GRMZM2G171390_T05
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171390_T05 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g41760.1 (Oryza sativa), 3'ss of exon 4
gtaactcagcacattcagcgtgtgtgtgtgtgtgcgtgcttgctcgcttaattacctgctgacaacctacgcgcattcaattctcatcagGTGCCAATCGACTGCTTCGAGGAGCAGTGGGTGATCTTCCGAGGCAAAGACGGAAGGCCCGGGTGTGTTCAGAACACATGCGCCCACAGGGCATGCCCGC
||||| ||    ||    |  |  | |     ||   |      |  ||||| |  || |        | | |   |   |  || |||||| ||||| || || || |||||||||||||| || |||||||| || || || || || || ||||||||||||||||| || ||||| || ||||| |
gtaacgcaatgaatgattcaggcatttaca-atgtccggagtaccagttaatgatatgtt-----ttgatgtggtctgtgtgttc-tcagGTACCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGATGGGAGACCTGGATGTGTTCAGAACACATGTGCTCACAGAGCCTGCCCTC

upper sequence: GRMZM2G171390_T05 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g41780.1 (Oryza sativa), 3'ss of exon 4
---gtaactcagcac-attcag-cgtgtgtgtgtgtgtgcgtgcttgctcgcttaattacctgctgacaacctacgcgcattcaattctcatcagGTGCCAATCGACTGCTTCGAGGAGCAGTGGGTGATCTTCCGAGGCAAAGACGGAAGGCCCGGGTGTGTTCAGAACACATGCGCCCACAGGGCATGCCCGC
     |||   |  | |||||| | | | | |  | |  |    ||    | |  |  | ||  ||   |  |       ||      |  |||||||||||| || || || |||||||||||||| || |||||||| || || || || || || ||||||  ||||||||| || ||||| || ||||| |
gtaaaaacaacgtgcgattcaggcatttttttacgaggtcagagttagcagttgcagaaacttatgtttatttgatgtggtttgcgcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGATGGGAGACCTGGATGTGTTATGAACACATGTGCTCACAGAGCTTGCCCTC

upper sequence: GRMZM2G171390_T05 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA04G42840.1 (Glycine max), 3'ss of exon 4
-gtaactcagcacattcagcgtgtgtgt---gtgtgtgcgtgcttgctcgcttaattacctgctgacaacct-acgcgcattcaa-----ttctcatcagGTGCCAATCGACTGCTTCGAGGAGCAGTGGGTGATCTTCCGAGGCAAAGACGGAAGGCCCGGGTGTGTTCAGAACACATGCGCCCACAGGGCATGCCCGC
  |  ||  |           | |||||    |  | |  | | ||  | |  |  |   ||   |    || | ||   || |      |  |  |||| | ||||| || || || ||||| |  ||||| ||||||||||| ||||| || | ||| ||||||||||||||||| || || ||||| ||||| || |
aatttcttggggtgacggagttctgtgtcagataagagactacctgtactccaatctggatgtaaattctcttaagcatgttaatccttttctttttcagATCCCAATAGAATGTTTTGAGGAACCATGGGTCATCTTCCGAGGGAAAGATGGGAAGCCTGGGTGTGTTCAGAACACCTGTGCACACAGAGCATGTCCTC

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|76290758|gb|DV030326.1|DV030326
EST:     TCTGGTACCCAGTCGCCTTCTCCAGCGATCTCAAGGCTCCTGACACCATG                         GTGCCAATCGACTGCTTCGAGGAGCAGTGGGTGATCTTCCGAGGCAAAGAC
genomic: TCTGGTACCCAGTCGCCTTCTCCAGCGATCTCAAGGCTCCTGACACCATGgtaactcagc ... ttctcatcagGTGCCAATCGACTGCTTCGAGGAGCAGTGGGTGATCTTCCGAGGCAAAGAC
EST: gi|91055542|gb|EB165960.1|EB165960
EST:     TCTGGTACCCAGTCGCCTTCTCCAGCGATCTCAAGGCTCCTGACACCATG                         GTGCCAATCGACTGCTTCGAGGAGCAGTGGGTGATCTTCCGAGGCAAAGAC
genomic: TCTGGTACCCAGTCGCCTTCTCCAGCGATCTCAAGGCTCCTGACACCATGgtaactcagc ... ttctcatcagGTGCCAATCGACTGCTTCGAGGAGCAGTGGGTGATCTTCCGAGGCAAAGAC
EST: gi|148944802|gb|EC889946.2|EC889946
EST:     TCTGGTACCCAGTCGCCTTCTCCAGCGATCTCAAGGCTCCTGACACCATG                         GTGCCAATCGACTGCTTCGAGGAGCAGTGGGTGATCTTCCGAGGCAAAGAC
genomic: TCTGGTACCCAGTCGCCTTCTCCAGCGATCTCAAGGCTCCTGACACCATGgtaactcagc ... ttctcatcagGTGCCAATCGACTGCTTCGAGGAGCAGTGGGTGATCTTCCGAGGCAAAGAC
EST: gi|71437528|gb|DR818578.1|DR818578
EST:     TCTGGTACCCAGTCGCCTTCTCCAGCGATCTCAAGGCTCCTGACACCATG                         GTGCCAATCGACTGCTTCGAGGAGCAGTGGGTGATCTTCCGAGGCAAAGAC
genomic: TCTGGTACCCAGTCGCCTTCTCCAGCGATCTCAAGGCTCCTGACACCATGgtaactcagc ... ttctcatcagGTGCCAATCGACTGCTTCGAGGAGCAGTGGGTGATCTTCCGAGGCAAAGAC
EST: gi|149014006|gb|EE043522.2|EE043522
EST:     TCTGGTACCCAGTCGCCTTCTCCAGCGATCTCAAGGCTCCTGACACCATG                         GTGCCAATCGACTGCTTCGAGGAGCAGTGGGTGATCTTCCGAGGCAAAGAC
genomic: TCTGGTACCCAGTCGCCTTCTCCAGCGATCTCAAGGCTCCTGACACCATGgtaactcagc ... ttctcatcagGTGCCAATCGACTGCTTCGAGGAGCAGTGGGTGATCTTCCGAGGCAAAGAC
EST: gi|78089256|gb|DV517630.1|DV517630
EST:     TCTGGTACCCAGTCGCCTTCTCCAGCGATCTCAAGGCTCCTGACACCATG                         GTGCCAATCGACTGCTTCGAGGAGCAGTGGGTGATCTTCCGAGGCAAAGAC
genomic: TCTGGTACCCAGTCGCCTTCTCCAGCGATCTCAAGGCTCCTGACACCATGgtaactcagc ... ttctcatcagGTGCCAATCGACTGCTTCGAGGAGCAGTGGGTGATCTTCCGAGGCAAAGAC
EST: gi|71447084|gb|DR828134.1|DR828134
EST:     TCTGGTACCCAGTCGCCTTCTCCAGCGATCTCAAGGCTCCTGACACCATG                         GTGCCAATCGACTGCTTCGAGGA
genomic: TCTGGTACCCAGTCGCCTTCTCCAGCGATCTCAAGGCTCCTGACACCATGgtaactcagc ... ttctcatcagGTGCCAATCGACTGCTTCGAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcttgctcgcttaattacctgctgacaacctacgcgcattcaattctcatcagGTGCCAATCGACTGCTTCGAGGAGCAGTGGGTGATCTTCCGAGGCAAAGACGGAAGGCCCGGGTGTGTTCAGAACACATGCGCCCACAGGGCATGCCCGC
                     tgctgac  putative branch site (score: 2)
                                             ttctcatc  putative PPT
            ttaatta  TA-rich tract