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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gccctgcaacgcaataacaatcgtatcatgtgtttggtgtcctacaatggtcgggtctgttgcttcttgtctttttgactccttgtgggatttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGAC

Basic information

species Zea mays
transcript GRMZM5G806449_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G806449_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g56850.1 (Oryza sativa), 3'ss of exon 2
-----gccctgcaacgcaataacaatcgtatcatgtgtttggtgtcctacaatggtcgggtctgttgcttcttgtctttttgactccttgtgggatttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGAC
      |  | |  | |     |  ||    ||| | |  |  |        |||     | | ||  ||| |||  ||| || ||  |||| |        |||||||||||||| |||||||| ||||| ||||||||||| || |||| |||||| |||||||||||
gtttgacttttctcctctcccccgctccc--catttttgcgaggaaacgtgttggatttttattttttttcgtgtgattt-gattcggtgtgtggcgcggttcagGTTGCGATTTGCGAGCTCCCGTTCCATCCCATCAGCTCGGATTGGCAAGGAGGGCATGGTGGGAC
















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|211339792|gb|FK980808.1|FK980808
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|211339790|gb|FK980806.1|FK980806
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|211339794|gb|FK980810.1|FK980810
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|33942501|gb|CF349101.1|CF349101
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|211339793|gb|FK980809.1|FK980809
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|211337407|gb|FK980805.1|FK980805
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|211339796|gb|FK980812.1|FK980812
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|211337405|gb|FK980803.1|FK980803
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|40485831|gb|CK394761.1|CK394761
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGTTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|33942302|gb|CF348902.1|CF348902
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|148945432|gb|EC890664.2|EC890664
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|211337397|gb|FK980795.1|FK980795
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|211337400|gb|FK980798.1|FK980798
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|148969995|gb|EE020910.2|EE020910
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|211337398|gb|FK980796.1|FK980796
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|148960879|gb|EE011558.2|EE011558
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|33101538|gb|CF061498.1|CF061498
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
EST: gi|111991059|gb|EE331961.1|EE331961
EST:     GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAG                         GTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA
genomic: GCAGCGGCGGCGTTCGCGGCTCTCGCACCGCCGCCTCCTTCGGAGCTAAGgttcgttgct ... tttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatggtcgggtctgttgcttcttgtctttttgactccttgtgggatttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGAC
                           ttttgac  putative branch site (score: 3)
                                             tttct  putative PPT
                        tcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gccctgcaacgcaataacaatcgtatcatgtgtttggtgtcctacaatggtcgggtctgttgcttcttgtctttttgactccttgtgggatttctggcagGTTGCGATTTGTGAGCTCCCATTCCACCCCATCAGCTCAGAGTGGCTAGGAGGACATGGTGGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- -ctgcaac
- - - - - - aataaca
- - - - - - - - - - - - - - tgtgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgttg