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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtgtgagccgccgccgtgcttaaaattttgagcttcttcccttccggggtgaaatgaaatgtccgatcgatgtgagagttcctttcttttttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGACGTGTACAGCTTCGGGATCCTGATCATGGAGATCATCTCCGGCCGAAGC

Basic information

species Zea mays
transcript GRMZM2G147051_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147051_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g36050.1 (Oryza sativa), 3'ss of exon 4
gtgggtgtgagccgccgccgtgcttaaaattttgagcttcttcccttccggggtgaaatgaaatgt--ccgatcgatgtgagagttcctttc--------ttttttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGACGTGTACAGCTTCGGGATCCTGATCATGGAGATCATCTCCGGCCGAAGC
      || ||  |  |  |||    |  || | |  |   ||    |||| |  |  | | ||||   |  |  |    |  ||  || |         || |   || | || || || || || |||||||| |||||||| |||||||| ||||| ||||| ||||||||||||||||||||||| ||||| ||||||||||| ||||||
------gtaagatg--gatgtg----aggttctcaattgtgtcgagcccggtgaaatgtaagatgtgagcactgaacactaaggtctctctggccatcgattctgcatttgcagTTATGTAGCACCGGAGTACGCGAGCACCGGGATGCTGAATGAGAGAAGCGATGTGTACAGCTTCGGGATCCTGATAATGGAAATCATCTCCGGTCGAAGC

upper sequence: GRMZM2G147051_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------gtgggtgtgagccgccgccgtgcttaaaattttgagcttcttcccttccggggtgaaatgaaatgt-ccgatcgatgtgagagttcctttc-----ttttttgttgga------agCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGACGTGTACAGCTTCGGGATCCTGATCATGGAGATCATCTCCGGCCGAAGC
                                             || | ||  ||       || || |  ||| | ||  |  |    |  |   ||   |||    ||     || | ||   ||| ||  ||     | ||| | || |      || ||||| ||||| |||||||| | ||| ||| ||||||| ||| | ||||| ||||||||||| ||| | ||  |||||||||||||| | || |||   
gtaagctcaaggccctcctctggattgtattgtattgttgaaacagtagttgc-agttataaacg-gcatttaatgtcgatttcttctagtcacatagttttatgtcgcgtgtttctcaacgttctagtccccatccccattctttggctgtatcactcagGTACGTAGCGCCGGAGTACGCGAACACGGGCCTGCTGAATGAGCGAAGCGATGTGTACAGCTTTGGGGTGCTTCTCATGGAGATCATCACGGGGCGAGAT

upper sequence: GRMZM2G147051_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ34699 (Selaginella moellendorffii), 3'ss of exon 4
gtgggtgtgagccgccgccgtgcttaaaattttgagcttcttcccttccggggtgaaatgaaatgtccgatcgatgtgagagttcctttcttttttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGACGTGTACAGCTTCGGGATCCTGATCATGGAGATCATCTCCGGCCGAAGC
                                        |   |   |     ||||    |  | |   |  | |  |  || |  | |||| |  |   || ||||| || || |||||||| ||||| ||| |||| ||||||||||||||||| || || |||||  ||||| |||||||  ||||  ||||  |   |
---------------------------------------gtaagcacgcaaatcgaaactccagatgcttacattctttgtttttcccttttttctcgtcacagATACGTTGCTCCCGAGTACGCAAGCACGGGCTTGCTCAACGAGAGGAGCGACGTCTATAGTTTCGGAGTCCTGCTCATGGAACTCATAACCGGAAGGGAC

upper sequence: GRMZM2G147051_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ31013 (Selaginella moellendorffii), 3'ss of exon 4
gtgggtgtgagccgccgccgtgcttaaaattttgagcttcttcccttccggggtgaaatgaaatgtccgatcgatgtgagagttcctttcttttttgttg--gaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGACGTGTACAGCTTCGGGATCCTGATCATGGAGATCATCTCCGGCCGAAGC
                                        |   |   |     ||||    |  | |   |  | |    |||  |  ||||||| | |    || ||||| || || |||||||| ||||| ||| |||| ||||||||||||||||| || || || ||  ||||| |||||||  ||||  ||||  |   |
---------------------------------------gtaagcaagcaaatcgaaactccagatgcttacattctttttgtttttcccttttttctcgtcacagATACGTTGCTCCCGAGTACGCAAGCACGGGCTTGCTCAACGAGAGGAGCGACGTCTATAGTTTTGGAGTCCTGCTCATGGAACTCATAACCGGAAGGGAC

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|71762919|gb|DR960856.1|DR960856
EST:     CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGG                         CTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
genomic: CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
EST: gi|71308371|gb|DR790412.1|DR790412
EST:     CTGGGGGCGGACAGCAACTACGTCACCCCCAGAGTGATGGGAACGTTTGG                         CTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
genomic: CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
EST: gi|71439998|gb|DR821048.1|DR821048
EST:     CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGG                         CTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
genomic: CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
EST: gi|31909329|gb|CD650864.1|CD650864
EST:     ACTACGTCACCACCAGAGTGATGGGAACGTTTGG                         CTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
genomic: ACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
EST: gi|30088116|gb|CB886321.1|CB886321
EST:     CACCACCAGAGTGATGGGAACGTTTGG                         CTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
genomic: CACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
EST: gi|31909517|gb|CD650958.1|CD650958
EST:     CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGG                         CTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
genomic: CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
EST: gi|28987043|gb|CB351436.1|CB351436
EST:     CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGG                         CTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
genomic: CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
EST: gi|71315686|gb|DR794464.1|DR794464
EST:     CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGG                         CTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
genomic: CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggggtgaaatgaaatgtccgatcgatgtgagagttcctttcttttttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGACGTGTACAGCTTCGGGATCCTGATCATGGAGATCATCTCCGGCCGAAGC
                                 ttcctttcttttttgt  CT-rich tract
                                     tttctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtgtgagccgccgccgtgcttaaaattttgagcttcttcccttccggggtgaaatgaaatgtccgatcgatgtgagagttcctttcttttttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGACGTGTACAGCTTCGGGATCCTGATCATGGAGATCATCTCCGGCCGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA