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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatacttgattgcctcttgccattacatgatgggttcccagttcccatactatttgtgtttgctgtactctgcatgtttcaagggtctgctttgcagttgcgggctttaaaacctttcctatccttgttatttcagTGGATTACCTCTTGTTCATGGTTCGTGACGTGAAGCTCGACCCGAATCCTGAAGAGGTGGCCGATGTCAAGTACATGAACCGGCATCAGCTGAAGGAGCT

Basic information

species Zea mays
transcript GRMZM2G133082_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133082_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g34180.1 (Oryza sativa), 3'ss of exon 5
gtacatacttgattgcctcttgccattacatgatgggttcccagttcccatactatttgtgtttgctgtactctgcatgtttcaagggtctgctt--tg-cagttgcgggctttaaaacctttcctatccttgttatttcagTGGATTACCTCTTGTTCATGGTTCGTGACGTGAAGCTCGACCCGAATCCTGAAGAGGTGGCCGATGTCAAGTACATGAACCGGCATCAGCTGAAGGAGCT
||| ||| |||    |||||  ||  ||| ||||   || | ||    ||||||  | ||    ||| |    ||| | ||       |    ||  || |  |||     |||| ||  |  ||     | |  ||||||||||| |||||| | |||||||||||||| ||| |||||  ||||||||||||||| |||||||| ||||||||| |||| ||  || ||||||||||| |
gtaaatatttgc---cctctgccctctacctgatacatttc-agccttcatacttatcgt-ccagctatcacttgcctcttgtgtattttcaattgctgtcttttgaaatttttagaatataaccatctttcgccatttcagTGGACTACCTCCTATTCATGGTTCGTGATGTGGAGCTCAGCCCGAATCCTGAAGAAGTGGCCGACGTCAAGTACGTGAATCGTGATGAGCTGAAGGAGTT
















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|50330295|gb|CO525421.1|CO525421
EST:     GAGGATGCTTTACAAGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGT                         TGGATTCCCTCTTGTTCATGGTTCGTGACGTGAAGCTCGACCCGAATCCTG
genomic: GAGGATGCTTTACAAGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGTgtacatactt ... gttatttcagTGGATTACCTCTTGTTCATGGTTCGTGACGTGAAGCTCGACCCGAATCCTG
EST: gi|71303302|gb|DR787754.1|DR787754
EST:     GCTTTACAAGGCTCCCTTCAGATGGAAAATGGGGCGAACACGAGT                         TGGATTACCTCTTGTTCATGGTTCGTGACGTGAAGCTCGACCCGAATCCTG
genomic: GCTTTACAAGGCT-CCTTCAGATGGAAAATGGGGCGAACACGAGTgtacatactt ... gttatttcagTGGATTACCTCTTGTTCATGGTTCGTGACGTGAAGCTCGACCCGAATCCTG
EST: gi|50335730|gb|CO530856.1|CO530856
EST:     GAGGATGCTTTACAAGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGT                         TGGATTACCTCTTGTTCATGGTTCGTGACGTGAAGCTCGACCCGAATCCTG
genomic: GAGGATGCTTTACAAGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGTgtacatactt ... gttatttcagTGGATTACCTCTTGTTCATGGTTCGTGACGTGAAGCTCGACCCGAATCCTG
EST: gi|67022742|gb|CO451491.1|CO451491
EST:     GAGGATGCTNTACAAGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGT                         TGGATTACCTNNCT-GT-CATGGTTCGTGNACGTGA-GCTCGACCCGAATC
genomic: GAGGATGCTTTACAAGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGTgtacatactt ... gttatttcagTGGATTACCT--CTTGTTCATGGTTCGTG-ACGTGAAGCTCGACCCGAATC
EST: gi|15312900|gb|BI478457.1|BI478457
EST:     GAGGATGCTTTACAAGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGT                         TGGATTACCTCTTGTTCATGGTTCGTGACGTGAAGCTCGACCCGAATCCTG
genomic: GAGGATGCTTTACAAGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGTgtacatactt ... gttatttcagTGGATTACCTCTTGTTCATGGTTCGTGACGTGAAGCTCGACCCGAATCCTG
EST: gi|154130380|gb|EC872179.2|EC872179
EST:     GAGGATGCTTTCCAAGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGT                         TGGATTACCTCTTGTTCATGGTTCGTGACGTGAAGCTCGACCCGAATCCTG
genomic: GAGGATGCTTTACAAGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGTgtacatactt ... gttatttcagTGGATTACCTCTTGTTCATGGTTCGTGACGTGAAGCTCGACCCGAATCCTG
EST: gi|71772753|gb|DR970679.1|DR970679
EST:     GAGGATGCTTTACAAGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGT                         TGGATTACCTCTTGTTCATGGTTCGTGACGTGAAGCTCGACCCGAATCCTG
genomic: GAGGATGCTTTACAAGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGTgtacatactt ... gttatttcagTGGATTACCTCTTGTTCATGGTTCGTGACGTGAAGCTCGACCCGAATCCTG
EST: gi|154130466|gb|EC872180.2|EC872180
EST:     GAGGATGCTTTACAAGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGT                         TGGATTACCTCTTGTTCATGGTTCGTGACGTGAAGCTCGACCCGAATCCTG
genomic: GAGGATGCTTTACAAGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGTgtacatactt ... gttatttcagTGGATTACCTCTTGTTCATGGTTCGTGACGTGAAGCTCGACCCGAATCCTG
EST: gi|32940743|gb|CF045562.1|CF045562
EST:     GAGGATGCTTTACAAGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGT                         TGGATTACCTCCTGTTCATGGTTCGTGACGTGAATCTCAACCCGAATCCTG
genomic: GAGGATGCTTTACAAGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGTgtacatactt ... gttatttcagTGGATTACCTCTTGTTCATGGTTCGTGACGTGAAGCTCGACCCGAATCCTG
EST: gi|71303304|gb|DR787755.1|DR787755
EST:     GAGGATGCTTTACAAGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGT                         TGGATTACCTCTTGTTCATGGTTCGTGACGTGAAGCTCGACCCGAATCCTG
genomic: GAGGATGCTTTACAAGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGTgtacatactt ... gttatttcagTGGATTACCTCTTGTTCATGGTTCGTGACGTGAAGCTCGACCCGAATCCTG
EST: gi|60354876|gb|DN221849.1|DN221849
EST:     GAGGATGCTTTACAAGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGT                         TGGATTACCTCTTGTTCATGGTTCGTGACGTGAAGCTCGACCCGAATCCTG
genomic: GAGGATGCTTTACAAGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGTgtacatactt ... gttatttcagTGGATTACCTCTTGTTCATGGTTCGTGACGTGAAGCTCGACCCGAATCCTG
EST: gi|71772754|gb|DR970680.1|DR970680
EST:     GAGGATGCTTTACAAGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGT                         TGGATTACCTCTTGTTCATGGTTCGTGACGTGAAGCTCGACCCGAATCCTG
genomic: GAGGATGCTTTACAAGGCTCCTTCAGATGGAAAATGGGGCGAACACGAGTgtacatactt ... gttatttcagTGGATTACCTCTTGTTCATGGTTCGTGACGTGAAGCTCGACCCGAATCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agggtctgctttgcagttgcgggctttaaaacctttcctatccttgttatttcagTGGATTACCTCTTGTTCATGGTTCGTGACGTGAAGCTCGACCCGAATCCTGAAGAGGTGGCCGATGTCAAGTACATGAACCGGCATCAGCTGAAGGAGCT
                               cctttcctatccttgt  CT-rich tract
                                           ttgttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatacttgattgcctcttgccattacatgatgggttcccagttcccatactatttgtgtttgctgtactctgcatgtttcaagggtctgctttgcagttgcgggctttaaaacctttcctatccttgttatttcagTGGATTACCTCTTGTTCATGGTTCGTGACGTGAAGCTCGACCCGAATCCTGAAGAGGTGGCCGATGTCAAGTACATGAACCGGCATCAGCTGAAGGAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT