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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttggattatatagtcgcaatgctttcgtcttccaaagcttggcaaatcttgactgattactgacgcgattacttcaactttgcag

Basic information

species Zea mays
transcript GRMZM2G044027_T02
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os03g16980.2 (Oryza sativa), 5'ss of exon 11
GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttggattatatagtcgcaatgctttcgtcttccaaagcttggcaaatcttgactgattactga-cgcgattacttcaactttgcag
|||||||||||||||||||||||||||||||||||||||||| ||| || || ||   || ||    | |     |||||  |  ||     |||  |  |  | || |       | |||  || ||||||
GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgtaagatgaat-atcctgttgccgaacatca---ttccatgggatgtt---tctgaatggcatgctaagtttccctgcttttaccttgcag
















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|32841175|gb|CD980856.1|CD980856
EST:     GTGAATTCACCATGCCGGAACTTGCTGAGAATGTGAAGGAG                         TTGATTAACCCAGATATAACAGTGACGATGACCG
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATTAACCCAGATATAACAGTGACGATGACCG
EST: gi|14206834|gb|BG840512.1|BG840512
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATTAACCCAGATATAACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATTAACCCAGATATAACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|32909997|gb|CF014809.1|CF014809
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATTAACCCAGATATAACAGTGACGATGACCG
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATTAACCCAGATATAACAGTGACGATGACCG
EST: gi|7216734|gb|AW562856.1|AW562856
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATTAACCCAGATATAACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATTAACCCAGATATAACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|211032180|gb|FL277400.1|FL277400
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATTAACCCAGATATAACA
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATTAACCCAGATATAACA
EST: gi|32850262|gb|CD989943.1|CD989943
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATTAACCCAGATATAACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATTAACCCAGATATAACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|32850554|gb|CD990235.1|CD990235
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATTAACCCAGATATAACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATTAACCCAGATATAACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|166541132|gb|EG308414.1|EG308414
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATTAAACCCAGATATAACAGTGACGATGACCGAGAACACTCC
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATTAA-CCCAGATATAACAGTGACGATGACCGAGAACACTCC
EST: gi|32866186|gb|CF005868.1|CF005868
EST:     GTGAACTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATTAACCCAGATATAACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATTAACCCAGATATAACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|32840626|gb|CD980307.1|CD980307
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGGGAAGGAG                         TTGATTAACCCAGATATAACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATTAACCCAGATATAACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|67013235|gb|CO441984.1|CO441984
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAANGGAG                         T-GATTAACCCAGATATAACAGTGACGATGACCGAGAACACTCCTGATGA
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAA-GGAGgcaagttgga ... aactttgcagTTGATTAACCCAGATATAACAGTGACGATGACCGAGAACACTCCTGATGA
EST: gi|213192508|gb|FM182601.1|FM182601
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATTAACCCAGATATAACAGTGACGATGACCGAGAACACTCCTGATGAT
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATTAACCCAGATATAACAGTGACGATGACCGAGAACACTCCTGATGAT
EST: gi|166419250|gb|EG304902.1|EG304902
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATTAACCCAGATATAACAGTGACGA
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATTAACCCAGATATAACAGTGACGA
EST: gi|166457737|gb|EG161293.1|EG161293
EST:     GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG                         TTGATTAACCCAGATATAACAGTGACGA
genomic: GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttgga ... aactttgcagTTGATTAACCCAGATATAACAGTGACGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAGgcaagttggattatatagtcgcaatgctttcgtcttccaaagcttggcaaatcttgactgattactgacgcgattacttcaactttgcag

- - - - -  ATGCTG
- - - - - -  GCTGGA
- - - - - - - - - - - - - - - - -  AAGGAG