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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtgacaacttgagaattaaattatgtgcacaagagccaataatcataagttattctgatttaacatgacattttttcagaataagttcacacgtcaccagtttggcaacacgttagaatgttgacaggtggtccctagctggcgttatcttatggttatgtgttgtcatttcagGTCCTCCACCATACTGTTTCCCTGGTTGCAATAGCTTACACAATGTTGTCTGGGGAAGGGCAGTTTTACACATACATGGTTCTCATTTCAGAGACAACCA

Basic information

species Zea mays
transcript GRMZM2G016184_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G016184_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g46410.1 (Oryza sativa), 3'ss of exon 5
gtaggtg---acaacttgagaat-taaattat-gtgcacaagagccaataatcataagttattctgatttaacatgacattttttcagaataagttcacacgtcaccagtttggcaacacgttagaatgttgacaggtggtccctagctggcgttatcttatggttatgtgttgtcatttcagGTCCTCCACCATACTGTTTCCCTGGTTGCAATAGCTTACACAATGTTGTCTGGGGAAGGGCAGTTTTACACATACATGGTTCTCATTTCAGAGACAACCA
||| |||   |  | |||   || || | |||  |  |  |     | |  | || | |||   | | ||||  | |  |||  |   |||||| |||  ||  |  | ||||||| || ||||||  |||   |||| || ||| | | ||  |||||||| ||| | | ||||  || ||| || |||| |||||| |||| || |||||||||||||||||||||||||| ||||| || ||||| ||||||||||||||||| |||||||| |||||||
gtatgtgttcagcatttgtctatatatactattataaattaagttaattgctaatgaattaggtttagttaaattta-gtttggtttcaataagctcatgcgata--attttggcagcatgttagacagtt---aggtagtgcctggttagcaatatcttattgttgtatattgtt-ttgcagATCGTCCATCATACTCTTTCTCTAGTTGCAATAGCTTACACAATGTTGTCAGGGGAGGGTCAGTTCTACACATACATGGTTCTTATTTCAGAAACAACCA

upper sequence: GRMZM2G016184_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv12s0028g01000.t01 (Vitis vinifera), 3'ss of exon 4
gtaggtgacaacttgagaattaaattatgtgcacaagagccaataatcataagttattctgatttaacatgacattttttcagaataagttcacacgtcaccagtttggcaacacgttagaatgttgacaggtggtccctagctggcgttatcttatggttatgtgttgtcatttcagGTCCTCCACCATACTGTTTCCCTGGTTGCAATAGCTTACACAATGTTGTCTGGGGAAGGGCAGTTTTACACATACATGGTTCTCATTTCAGAGACAACCA
                                                                          |  |    |     ||              | |   |||  ||   | |    ||  |   |   | | ||| |  |||       |     ||||||||||||||  | || |||  | | ||  | | |||| | || ||  |||||||| |||||||||||||  ||||||| ||||||||||| || || |||||||| |
-------------------------------------------------------------------------gtggtggaggtgggggtgggaggaaagttgatgttttaacttgtagaagtaaaaacttgaaat---tggttgg-gaaatcaaggcactg-acattgtcatttcagGTGGTTCATCATCTTTTATCTATAGCTGCAGTGGCATATGCAATGTTGACTGGGGAAGGGCAACTTTACACCTACATGGTTCTTATCTCTGAGACAACAA
















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|60355201|gb|DN222174.1|DN222174
EST:     ATCTTGCAATGATCTTCTGGCTGTATCCTTCCCTTGGTGGAATGGAATAT                         GTCCTCCACCATACTGTTTCCCTGGTTGCAATAGCTTACACAATGTTGTCT
genomic: ATCTTGCAATGATCTTCTGGCTGTATCCTTCCCTTGGTGGAATGGAATATgtaggtgaca ... gtcatttcagGTCCTCCACCATACTGTTTCCCTGGTTGCAATAGCTTACACAATGTTGTCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgacaggtggtccctagctggcgttatcttatggttatgtgttgtcatttcagGTCCTCCACCATACTGTTTCCCTGGTTGCAATAGCTTACACAATGTTGTCTGGGGAAGGGCAGTTTTACACATACATGGTTCTCATTTCAGAGACAACCA
 tgttgac  putative branch site (score: 3)
                                              tcatttc  putative PPT
                         ttatcttat  TA-rich tract