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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccctgactaggggttgtgagcatgaaaaattgcttacgccacagtttgtggtcttcccgtatggctgcaattgtatttacgtgaactggctcttttgcagCCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGTCCAAGAGGGTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAG

Basic information

species Zea mays
transcript GRMZM2G174204_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174204_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g47580.1 (Oryza sativa), 3'ss of exon 3
---ccctgactaggggttgtgagcatgaaaaattgcttacgccacagtttgtggtcttcccgtatggctgcaattgtatttacgtgaactggctcttttgcagCCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGTCCAAGAGGGTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAG---
      ||| |  | | ||||||||| | || | ||    |  | | ||  | || |    | ||  ||| ||  ||   | |  | |   |  |  ||||||||||||||||||||| || |||| |   || ||||||||||||||||   | |||||||||||||||||||| ||||| ||||| ||||||||||||||    
atattttgattgtgagatgtgagcattataattcgcaagtgtaaaatttgcttgtttggttgcatttctgtaaa-gttcattcacggat--gtacacttgcagCCTGAAAATGCACGACGAGTCAACTTCTCGGCAGAAGGTTGATGATG---TTCAAGAGGGTGCTCTTCCTCCATATCTGCTGGACCGTGATCAGACACAACGT
















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|8366902|gb|BE049910.1|BE049910
EST:     AAACGCTATGCTGAGAAGGCGCAGATGAAGAAGAC                         CCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTGGATGATGATGT
genomic: AAACGCTATGCTGAGAAGGCGCAGATGAAGAAGACgtaagtgctt ... tcttttgcagCCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
EST: gi|78109120|gb|DV527537.1|DV527537
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGAC                         CCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGACgtaagtgctt ... tcttttgcagCCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
EST: gi|37398604|gb|CF636617.1|CF636617
EST:     AGAGGTTTCGCCAAGAAACGCTATGCTGAGAAGCCGCAGATGAAGAAGAC                         CCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
genomic: AGAGG-TTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGACgtaagtgctt ... tcttttgcagCCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
EST: gi|71440545|gb|DR821595.1|DR821595
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGAC                         CCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGACgtaagtgctt ... tcttttgcagCCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
EST: gi|211464729|gb|FL207495.1|FL207495
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGAC                         CCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGACgtaagtgctt ... tcttttgcagCCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
EST: gi|211464737|gb|FL207503.1|FL207503
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGAC                         CCTGAAAATNCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGACgtaagtgctt ... tcttttgcagCCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
EST: gi|211464734|gb|FL207500.1|FL207500
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGAC                         CCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGACgtaagtgctt ... tcttttgcagCCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
EST: gi|14883663|gb|BI273476.1|BI273476
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGAC                         CCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGACgtaagtgctt ... tcttttgcagCCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
EST: gi|149079698|gb|EE168699.2|EE168699
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGAC                         CCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGACgtaagtgctt ... tcttttgcagCCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
EST: gi|211464740|gb|FL207506.1|FL207506
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGAC                         CCTGAAAATGCA
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGACgtaagtgctt ... tcttttgcagCCTGAAAATGCA
EST: gi|15053622|gb|BI359167.1|BI359167
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGAC                         CCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGACgtaagtgctt ... tcttttgcagCCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
EST: gi|211464732|gb|FL207498.1|FL207498
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGAC                         CCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGACgtaagtgctt ... tcttttgcagCCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
EST: gi|71440546|gb|DR821596.1|DR821596
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGAC                         CCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGACgtaagtgctt ... tcttttgcagCCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
EST: gi|148933462|gb|EC877158.2|EC877158
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGAC                         CCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGACgtaagtgctt ... tcttttgcagCCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
EST: gi|15053623|gb|BI359168.1|BI359168
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGAC                         CCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGACgtaagtgctt ... tcttttgcagCCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
EST: gi|50332541|gb|CO527667.1|CO527667
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGAC                         CCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGACgtaagtgctt ... tcttttgcagCCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
EST: gi|22545768|gb|BU098142.1|BU098142
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGACgtaagtgctt ... tcttttgcagCCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
EST: gi|31359359|gb|CD443716.1|CD443716
EST:     AAGAGGGTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGAC                         CCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGGTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGACgtaagtgctt ... tcttttgcagCCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
EST: gi|211462211|gb|FL207488.1|FL207488
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGACgtaagtgctt ... tcttttgcagCCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
EST: gi|211464730|gb|FL207496.1|FL207496
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGAC                         CCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGACgtaagtgctt ... tcttttgcagCCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
EST: gi|15313826|gb|BI478973.1|BI478973
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGAC                         CCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGACgtaagtgctt ... tcttttgcagCCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
EST: gi|211462214|gb|FL207491.1|FL207491
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGACgtaagtgctt ... tcttttgcagCCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
EST: gi|76917038|gb|DV166648.1|DV166648
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGAC                         CCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGACgtaagtgctt ... tcttttgcagCCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
EST: gi|22819549|gb|BU499639.1|BU499639
EST:     AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGAC                         CCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT
genomic: AAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGACgtaagtgctt ... tcttttgcagCCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtggtcttcccgtatggctgcaattgtatttacgtgaactggctcttttgcagCCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGTCCAAGAGGGTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAG
                                            ctcttttgc  CT-rich tract
                       aattgtattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccctgactaggggttgtgagcatgaaaaattgcttacgccacagtttgtggtcttcccgtatggctgcaattgtatttacgtgaactggctcttttgcagCCTGAAAATGCACGATGAATCAAATAAGCGACAGAAGGTTGATGATGATGTCCAAGAGGGTGCTCTTCCTCCGTATCTACTGGATCGTGATCAGACACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - -gcatgaa
- - - - - - - - - - - - - - - tgcttac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaactg