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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCACGGCTGGCTGCAATTGACTTCATTGTTTGTGATGAGAGTGATGTCTTTGTTACGAATAATAATGGGAACATGGCCAAAGTTTTAGCTGGACGGAGgtatgtacccctctttttctgcatatgctttgggtattctaaactaatccctccatcccaaataaatcaactcccctagaatgacccagagtaaaattat...

Basic information

species Zea mays
transcript GRMZM2G101181_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101181_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os04g46570.1 (Oryza sativa), 5'ss of exon 8
CTTCACGGCTGGCTGCAATTGACTTCATTGTTTGTGATGAGAGTGATGTCTTTGTTACGAATAATAATGGGAACATGGCCAAAGTTTTAGCTGGACGGAGgtatgtacccctctttttctgcatatgctttgggtattctaaactaatccctccatcccaaataaat---caactcccctagaatgacccagagtaaaattat
||||| |  ||||||||||||| ||||| || ||||| | ||||||||| |||||||| || |||||||| ||||||||||| |||||||||||||| ||||||| | |  |||| |  || || ||||     | |||||||   |        |   |  ||||     ||  |  |  | ||||  || |   |  | ||
CTTCAAGATTGGCTGCAATTGATTTCATCGTATGTGACGGGAGTGATGTTTTTGTTACAAACAATAATGGAAACATGGCCAAGGTTTTAGCTGGACGAAGgtatgcatctatcttctaatggatttgct--aaatgttctaaatgtaaagtatagttgaatgtaaacagataagccttcaggtatgatgca-atccacctgat

upper sequence: GRMZM2G101181_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA01G41740.1 (Glycine max), 5'ss of exon 8
CTTCACGGCTGGCTGCAATTGACTTCATTGTTTGTGATGAGAGTGATGTCTTTGTTACGAATAATAATGGGAACATGGCCAAAGTTTTAGCTGGACGGAGgta------tgtacccctctttttctgcatatgctttgggtattc--taaactaatccctccatcccaaataaatcaactcccctagaatgacccagagtaaaattat
|||| || || ||||| ||||||| ||||||||||||||| |||||||| |||||||| || || ||||| |||||||||||  || | || || || |||||      | ||       |||  |        ||||  | ||   || | ||||      ||  | || || | ||      || ||||| | | | ||       
CTTCCCGCCTTGCTGCTATTGACTACATTGTTTGTGATGAAAGTGATGTATTTGTTACTAACAACAATGGTAACATGGCCAAGATTCTTGCAGGTCGAAGgtaataatatataaaatctctttaatatcctccttttgtttgtttagtacattaatgaacttatttctaa-aagttaaactaaatacaatgaac-aaactat------

upper sequence: GRMZM2G101181_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA17G15170.1 (Glycine max), 5'ss of exon 8
CTTCACGGCTGGCTGCAATTGACTTCATTGTTTGTGATGAGAGTGATGTCTTTGTTACGAATAATAATGGGAACATGGCCAAAGTTTTAGCTGGACGGAGgta----tgtacccctctttt--tctgcatatgctttgggtattctaaactaatccctccatcccaaataaat--caactcccctagaatgacccagagta-aaattat
|||| || || ||||| ||||||| ||||||||||||||| ||| |||| |||||||| || |||||||| |||||||||||| |  | || || || |||||    || |  | |  | |  ||    ||| |||    |||  | ||  |||   | |     |  |   |  || || |  || |    |  |  ||| |||  | 
CTTCCCGCCTTGCTGCTATTGACTACATTGTTTGTGATGAAAGTAATGTATTTGTTACTAACAATAATGGTAACATGGCCAAAATCCTTGCCGGTCGAAGgtaataatgaatgcatggtgtcatccttttattcttcctttatgtttaaaaaatttatacgattaatgtgtttggcatctactataaacctgctgattgtacaaaacag

upper sequence: GRMZM2G101181_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA05G04720.1 (Glycine max), 5'ss of exon 8
CTTCACGGCTGGCTGCAATTGACTTCATTGTTTGTGATGAGAGTGATGTCTTTGTTACGAATAATAATGGGAACATGGCCAAAGTTTTAGCTGGACGGAGgtatg-------------tacccctcttt--ttctgcat--atgctttgggtattctaaactaatccctccatcccaaataaatcaactcccctagaatgacccagagtaaaattat
|||| || || ||||| ||||||| ||| ||||||||||| ||| |||| ||||| || || || ||||| |||||||||||| |  | ||||| || ||||| |             | ||   ||||  |||| | |  ||| ||     | |   |    ||    |  |      |  |  | |  || |    |      |   ||||    
CTTCCCGCCTTGCTGCTATTGACTACATCGTTTGTGATGAAAGTAATGTATTTGTCACTAACAACAATGGTAACATGGCCAAAATCCTTGCTGGTCGTAGgtaagaatgaatacatgatgccatcctttaattcttcctttatgtttcaaaaaatgatatacgattaacctgttttcctttgactatcaaccttctgttctgattgtacaaaacag-

upper sequence: GRMZM2G101181_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA11G03640.1 (Glycine max), 5'ss of exon 9
CTTCACGGCTGGCTGCAATTGACTTCATTGTTTGTGATGAGAGTGATGTCTTTGTTACGAATAATAATGGGAACATGGCCAAAGTTTTAGCTGGACGGAGgta------tgtacccctctttttctgcatatgctttgggtattc--taaactaatccctccatcccaaataaatcaactcccctagaatgacccagagtaaaattat
|||| || || ||||| ||||||| ||||||||||||||| |||||||| |||||||| || || ||||| |||||||| ||  || | || || || |||||      | ||      ||||  |        ||||  | ||   || | | ||      ||  | || || | ||      || ||||| |       |||||||
CTTCCCGCCTTGCTGCTATTGACTACATTGTTTGTGATGAAAGTGATGTATTTGTTACTAACAACAATGGTAACATGGCAAAGATTCTCGCAGGTCGAAGgtaataatatataaaatctttttaatatcctccttttgtttgtttaatacattgatgaacttatttctaa-aagttaaactaaatacaatgaac-------aaattat

upper sequence: GRMZM2G101181_T01 (Zea mays), 5'ss of exon 8
lower sequence: AT4G16650.1 (Arabidopsis thaliana), 5'ss of exon 8
CTTCACGGCTGGCTGCAATTGACTTCATTGTTTGTGATGAGAGTGATGTCTTTGTTACGAATAATAATGGGAACATGGCCAAAGTTTTAGCTGGACGGAGgta----tgtacccctctttttctgcatatgctttgggtattctaaactaatccctccatcccaaataaatcaactcccctagaatgacccagagtaaaattat
||||||| || ||||| ||||||| ||||||| |||| || || ||||| ||| | || ||||||||||| || ||||||||  || | || || || |||||    | |   || ||| | |    ||    || | | ||  |||||  |   ||||   | ||  ||    |      |   | | |    || |  ||  
CTTCACGCCTTGCTGCCATTGACTACATTGTTAGTGACGAAAGCGATGTGTTTATCACTAATAATAATGGAAATATGGCCAAGATTCTTGCAGGCCGAAGgtaaggatattttccacttgtccccattaaagatttgctgttaaaaactgtt--ttccagtacgaaacaacaggcgatagcatc-ttatcatctgttactttg-

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|76282455|gb|DV022023.1|DV022023
EST:     TTTGTTACGAATAATAATGGGAACATGGCCAAAGTTTTAGCTGGACGGAG                         GGGATACATGGGCCACAAGAGAACTATTCGCCCAAATGCAAAGAAACTCAA
genomic: TTTGTTACGAATAATAATGGGAACATGGCCAAAGTTTTAGCTGGACGGAGgtatgtaccc ... aaatgtgtagGCGATACATGGGCCACAAGAGAACTATTCGCCCAAATGCAAAGAAACTCAA
EST: gi|5713681|gb|AI943673.1|AI943673
EST:     TTTGTTACGAATAATAATGGGAACATGGCCAAAGTTTTAGCTGGACGGAG                         GCGATACATGGGCCCCAAGAGAACTATTCGCCCAAATGCAAAGAAACTCAA
genomic: TTTGTTACGAATAATAATGGGAACATGGCCAAAGTTTTAGCTGGACGGAGgtatgtaccc ... aaatgtgtagGCGATACATGGGCCACAAGAGAACTATTCGCCCAAATGCAAAGAAACTCAA
EST: gi|78025385|gb|DV493772.1|DV493772
EST:     TTTGTTACGAATAATAATGGGAACATGGCCAAAGTTTTAGCTGGACGGAG                         GCGATACATGGGCCACAAGAGAACTATTCGCCCAAATGCAAAGAAACTCAA
genomic: TTTGTTACGAATAATAATGGGAACATGGCCAAAGTTTTAGCTGGACGGAGgtatgtaccc ... aaatgtgtagGCGATACATGGGCCACAAGAGAACTATTCGCCCAAATGCAAAGAAACTCAA
EST: gi|148935746|gb|EC879790.2|EC879790
EST:     TTTGTTACGAATAATAATGGGAACATGGCCAAAGTTTTAGCTGGACGGAG                         GCGATACATGGGCCACAAGAGAACTATTCGCCCAAATGCAAAGAAACTCAA
genomic: TTTGTTACGAATAATAATGGGAACATGGCCAAAGTTTTAGCTGGACGGAGgtatgtaccc ... aaatgtgtagGCGATACATGGGCCACAAGAGAACTATTCGCCCAAATGCAAAGAAACTCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCACGGCTGGCTGCAATTGACTTCATTGTTTGTGATGAGAGTGATGTCTTTGTTACGAATAATAATGGGAACATGGCCAAAGTTTTAGCTGGACGGAGgtatgtacccctctttttctgcatatgctttgggtattctaaactaatccctccatcccaaataaatcaactcccctagaatgacccagagtaaaattat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctccatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagtaaaa