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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagatctctgctcagttttctcacttttttttcctagtaccagtctggtaattatttttctaacatcacactttttttagGGGGAAGCATTGTTTCAGACACATGAGAATCTGGAACACCTAGCAATGATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAG

Basic information

species Zea mays
transcript GRMZM2G366935_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G366935_T09 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 8
gttagatctctgctcagttttctcacttttttttcctagtaccagtctggtaattatttttctaacatcacactttttttagGGGGAAGCATTGTTTCAGACACATGAGAATCTGGAACACCTAGCAATGATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAG
||| ||| |||  |||   | |  | ||||  || ||  ||||    | |    ||| || |||||   | |     |||||||||||||||||||||| ||||||||||| || || ||| |||||||||||||||| |||||||| || || ||||| || |||||| ||||| | ||
gtttgatatcttgtca---tgcatatttttcctttcttttacc---ttagc--ctatgttcctaaccataaaaaacctttagGGGGAAGCATTGTTTCAAACACATGAGAACCTTGAGCACTTAGCAATGATGGAGAGGGTTTTGGGTCCACTCCCAGAACACATGATAAGGAAAGCCAG

upper sequence: GRMZM2G366935_T09 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA06G08480.1 (Glycine max), 3'ss of exon 9
------gttagatctctgctcagttttctca--cttttttttcctagtaccagtctggtaattatttttctaacatc-acactttttttagGGGGAAGCATTGTTTCAGACACATGAGAATCTGGAACACCTAGCAATGATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAG
       ||  || |||    |  | | | |  | |   ||   ||        || ||  |  | ||   ||  |  | ||||||   |||| ||||||||||||||||| ||||| ||  |||| ||||| ||||||||||| ||||||||||||||| | ||||||||||||||  | |  || | 
gtttgtcttccatatctatcaatatgtattaggcatggcttgaatatggaacaactagtcttagtgttctaaatgtggaaacttttgacagGGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAA

upper sequence: GRMZM2G366935_T09 (Zea mays), 3'ss of exon 8
lower sequence: Vv04s0008g04220.t01 (Vitis vinifera), 3'ss of exon 9
gttagatctc---tgctcagttttctca--cttttttttccta-gtaccagtctggtaattatttttctaacat-cacactttttttagGGGGAAGCATTGTTTCAGACACATGAGAATCTGGAACACCTAGCAATGATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAG
|| ||  | |   |  || | | | | |  |  | || |  || | | || | || | |  | |  |  |   |  | | ||||   |||| |||||||| |||||||||||||||||  |||| ||  | || ||||||||||| || ||||||||||| |||||||||||||| ||||   ||||
gtcagtccccacttattctgatgtattaagccctgttgtgatatggaacattgtgatcagaactcctaaactgtgtataattttgacagGGTGAAGCATTATTTCAGACACATGAGAACTTGGAGCATTTGGCCATGATGGAGAGGGTGTTGGGACCTCTGCCAGAGCATATGATTCGGAGGGCAAG

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|71426269|gb|DR807319.1|DR807319
EST:     TTCCATGTGATATTTGGAGTGTTGGCTGTATTCTTGTTGAACTATGCTCT                         GGGGAAGCATTGTTTCAGACACATGAGAATCTGGAACACCTAGCAATGATG
genomic: TTCCATGTGATATTTGGAGTGTTGGCTGTATTCTTGTTGAACTATGCTCTgttagatctc ... ctttttttagGGGGAAGCATTGTTTCAGACACATGAGAATCTGGAACACCTAGCAATGATG
EST: gi|71766680|gb|DR964617.1|DR964617
EST:     TTCCATGTGATATTTGGAGTGTTGGCTGTATTCTTGTTGAACTATGCTCT                         GGGGAAGCATTGTTTCAGACACATGAGAATCTGGAACACCTAGCAATGATG
genomic: TTCCATGTGATATTTGGAGTGTTGGCTGTATTCTTGTTGAACTATGCTCTgttagatctc ... ctttttttagGGGGAAGCATTGTTTCAGACACATGAGAATCTGGAACACCTAGCAATGATG
EST: gi|76915207|gb|DV165881.1|DV165881
EST:     GTGATATTTGGAGTGTGGGCTGTATTTTTGTTGAACTATGCTTT                         GGGGAAGCATTGTTTCAGACACATGAGAATCTGGAACACCTAGCAATGATG
genomic: GTGATATTTGGAGTGTTGGCTGTATTCTTGTTGAACTATGCTCTgttagatctc ... ctttttttagGGGGAAGCATTGTTTCAGACACATGAGAATCTGGAACACCTAGCAATGATG
EST: gi|24765506|gb|CA400665.1|CA400665
EST:     TACCATGTGATATTTGGAGTGTTGGCTGTATTCTTGTTGAACTATGCTCT                         GGGGAAGCATTGTTTCAGACACATGAGAATCTGGAACACCTAGCAATGATG
genomic: TTCCATGTGATATTTGGAGTGTTGGCTGTATTCTTGTTGAACTATGCTCTgttagatctc ... ctttttttagGGGGAAGCATTGTTTCAGACACATGAGAATCTGGAACACCTAGCAATGATG
EST: gi|74242829|gb|DT650743.1|DT650743
EST:     TTCCATGTGATATTTGGAGTGTTGGCTGTATTCTTGTTGAACTATGCTCT                         GGGGAAGCATTGTTTCAGACACATGAGAATCTGGAACACCTAGCAATGATG
genomic: TTCCATGTGATATTTGGAGTGTTGGCTGTATTCTTGTTGAACTATGCTCTgttagatctc ... ctttttttagGGGGAAGCATTGTTTCAGACACATGAGAATCTGGAACACCTAGCAATGATG
EST: gi|71775054|gb|DR972932.1|DR972932
EST:     TTCCATGTGATATTTGGAGTGTTGGCTGTATTCTTGTTGAACTATGCTCT                         GGGGAAGCATTGTTTCAGACACATGAGAATCTGGAACACCTAGCAATGATG
genomic: TTCCATGTGATATTTGGAGTGTTGGCTGTATTCTTGTTGAACTATGCTCTgttagatctc ... ctttttttagGGGGAAGCATTGTTTCAGACACATGAGAATCTGGAACACCTAGCAATGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttcctagtaccagtctggtaattatttttctaacatcacactttttttagGGGGAAGCATTGTTTCAGACACATGAGAATCTGGAACACCTAGCAATGATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAG
                                ttctaac  putative branch site (score: 1)
                                           cacttttttt  putative PPT
                       taattatttttctaac  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagatctctgctcagttttctcacttttttttcctagtaccagtctggtaattatttttctaacatcacactttttttagGGGGAAGCATTGTTTCAGACACATGAGAATCTGGAACACCTAGCAATGATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA