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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcttgctgaattcagattacaaattgtgaactctacccatgcaggcactagctatttcacttttgatactgtgtggtcctgtggacagtccgagtaatgcatgcacgtactctgatgaaacagGCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTCAAGGTCTCTTTCCAGATTGAAGAACCAGTTCCAAGCTGGAAAGGGCATG

Basic information

species Zea mays
transcript GRMZM2G158627_T03
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158627_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os06g43760.1 (Oryza sativa), 3'ss of exon 25
gtaagtcttgctgaattcagattacaaattgtgaactctacccatgcaggcactagctatttcacttttgatactgtgtggtcctgtggacagtccgagtaatgcatgcacgtactctgatgaaacagGCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTCAAGGTCTCTTTCCAGATTGAAGAACCAGTTCCAAGCTGGAAAGGGCATG
           | ||| ||   |  |  |  |    | |||   |  |     | | | ||    | |||  | | | |  |  | |   | |   | ||||   | |    |||| ||||| |||||||||  |  | ||| | || || || | ||||||| | |||||||||||| ||||||||||||||||  | ||||| ||||| || |||| |
----------gtaaatacaacct-tatctgatagggtgtacttgtcta--ttttcgttgttaatgtcttggcattctctt-tgttatattctgcatg-gtaacataagtgtctactttgatggaacagGCAACCGTGAGCATTTTGATGCATTAAAAGTATATTTACTGTCAAGGTCTATTTCCAGATTGAAGAATGAATTCCAGGCTGGGAATGGCAAG
















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|40334151|gb|CK368221.1|CK368221
EST:     TGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATGCCTCAG                         GCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTC
genomic: TGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATGCCTCAGgtaagtcttg ... gatgaaacagGCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTC
EST: gi|67025030|gb|CO453779.1|CO453779
EST:     TGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATGCCTCAG                         GCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTCAAGGTCTC
genomic: TGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATGCCTCAGgtaagtcttg ... gatgaaacagGCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTCAAGGTCTC
EST: gi|5499479|gb|AI855346.1|AI855346
EST:     TGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATGCCTCAG                         GCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCT
genomic: TGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATGCCTCAGgtaagtcttg ... gatgaaacagGCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCT
EST: gi|45568479|gb|CK986083.1|CK986083
EST:     TGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATGCCTCAG                         GCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTCAAGGTCTC
genomic: TGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATGCCTCAGgtaagtcttg ... gatgaaacagGCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTCAAGGTCTC
EST: gi|74240586|gb|DT648500.1|DT648500
EST:     TGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATGCCTCAA                         GCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTCAAGGTCTC
genomic: TGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATGCCTCAGgtaagtcttg ... gatgaaacagGCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTCAAGGTCTC
EST: gi|60345148|gb|DN212121.1|DN212121
EST:     TGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATGCCTCAG                         GCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTCAAGGTCTC
genomic: TGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATGCCTCAGgtaagtcttg ... gatgaaacagGCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTCAAGGTCTC
EST: gi|37373885|gb|CF623267.1|CF623267
EST:     TGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATGCCTCAG                         GCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTCAAGGTCTC
genomic: TGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATGCCTCAGgtaagtcttg ... gatgaaacagGCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTCAAGGTCTC
EST: gi|113702485|gb|EE679989.1|EE679989
EST:     TGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATGCCTCAG                         GCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTCAAGGTCTC
genomic: TGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATGCCTCAGgtaagtcttg ... gatgaaacagGCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTCAAGGTCTC
EST: gi|78022271|gb|DV490658.1|DV490658
EST:     TGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATGCCTCAG                         GCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTCAAGGTCTC
genomic: TGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATGCCTCAGgtaagtcttg ... gatgaaacagGCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTCAAGGTCTC
EST: gi|78109267|gb|DV527683.1|DV527683
EST:     CTTTCTCATGCCTCAG                         GCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTCAAGGTCTC
genomic: CTTTCTCATGCCTCAGgtaagtcttg ... gatgaaacagGCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTCAAGGTCTC
EST: gi|211108629|gb|FL325826.1|FL325826
EST:     GCAAGGTCCACCCCTATTTCTTGCACCATATCTTCTTTCTCATGCCTCAG                         GCAAAAGCAATCATGTGGAGGCGTTGAGGAGTATAT
genomic: GCAAGGTCCACCCCTATT-CTTGCACCAGATCTTCTTTCTCATGCCTCAGgtaagtcttg ... gatgaaacagGCAAAAGCAATCATGTGGAGGCGTTGAG-AGTATAT
EST: gi|71432888|gb|DR813938.1|DR813938
EST:     TGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATGCCTCAA                         GCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTCAAGGTCTC
genomic: TGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATGCCTCAGgtaagtcttg ... gatgaaacagGCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTCAAGGTCTC
EST: gi|60337676|gb|DN204649.1|DN204649
EST:     TGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATGCCTCAG                         GCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTCAAGGTCTC
genomic: TGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATGCCTCAGgtaagtcttg ... gatgaaacagGCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTCAAGGTCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtgtggtcctgtggacagtccgagtaatgcatgcacgtactctgatgaaacagGCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTCAAGGTCTCTTTCCAGATTGAAGAACCAGTTCCAAGCTGGAAAGGGCATG
                                         ctctgat  putative branch site (score: 4)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcttgctgaattcagattacaaattgtgaactctacccatgcaggcactagctatttcacttttgatactgtgtggtcctgtggacagtccgagtaatgcatgcacgtactctgatgaaacagGCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTCAAGGTCTCTTTCCAGATTGAAGAACCAGTTCCAAGCTGGAAAGGGCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA