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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTGCTGTGGTTAGCAAATTGCACAAACTTATCAACTGTAATGGTGGTGTAACATATATACATTGTACTGCTGGACTTGGAAGAGCTCCTGCTGTTGCAgtaggtttacatgccacccccccctaatttttgtttcccaagacaacttattgtttcacagattccttatgtttgtctagagatccttttgcttcagtag...

Basic information

species Zea mays
transcript GRMZM2G052546_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052546_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os03g01750.2 (Oryza sativa), 5'ss of exon 8
TCCTGCTGTGGTTAGCAAATTGCACAAACTTATCAACTGTAATGGTGGTGTAACATATATACATTGTACTGCTGGACTTGGAAGAGCTCCTGCTGTTGCAgtaggtttacatgccacccccccctaatttttgtttcccaagacaacttattgt---ttcacagattccttatgtttgtctagagatccttttgcttcagtag--
|||||||||| |||||||| ||||||| ||| |||||  ||||||||| |||||||||||||| ||||| ||||||||||| ||||||||||||||  |||||||||| ||||       |      ||||||||||||||||   |||||  |   || |    | | ||||  |  | |     || ||    ||||||    
TCCTGCTGTGATTAGCAAACTGCACAAGCTTGTCAACCATAATGGTGGGGTAACATATATACACTGTACCGCTGGACTTGGGAGAGCTCCTGCTGTGACAgtaggtttccatggtcttttct-----tttttgtttcccaagaattcttataataggtttaggtttacattataatattgtcttcttctttcctgttcagttagt

upper sequence: GRMZM2G052546_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA20G33190.1 (Glycine max), 5'ss of exon 8
TCCTGCTGTGGTTAGCAAATTGCACAAACTTATCAACTGTAATGGTGGTGTAACATATATACATTGTACTGCTGGACTTGGAAGAGCTCCTGCTGTTGCAgtaggtttacatgccacccccccctaatttttgtttcccaagacaacttattgtttcacagattccttatgtttgtctagagatccttttgcttcagtag-----
||| | ||| |||||||||||  ||||    || || |  ||||| |||||||||||||||||||| ||||||||||||||||||||||| |||||||| ||| || |    |   |       | ||    ||| | ||   ||   |||| |  |  | ||   || |||| ||   | | |    |      | ||      
TCCAGTTGTAGTTAGCAAATTATACAAGGCAATAAATTCCAATGGAGGTGTAACATATATACATTGCACTGCTGGACTTGGAAGAGCTCCAGCTGTTGCGgtatgtctcttagtttcttttatgtgatgcaagttactca---cagaatatt-tacctgaaatgttttttgttagttctg-ggtaaggtaaaggaaataatttcc

upper sequence: GRMZM2G052546_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA10G34370.2 (Glycine max), 5'ss of exon 7
TCCTGCTGTGGTTAGCAAATTGCACAAACTTATCAACTGTAATGGTGGTGTAACATATATACATTGTACTGCTGGACTTGGAAGAGCTCCTGCTGTTGCAgtaggtttacatgccacccccccctaatttttgtttcccaagacaacttattgtttcacagattccttatgtttg-tctagagatccttttgcttcagtag-----
||| ||||| |||||||||||  ||||    || || |  ||||| |||||||||||||||||||| ||||||||||||||||||||||| |||||||| ||| || |    |   |       | ||    ||| | ||   ||   |||| |  |  | ||   ||  ||| | |||||  |   |   |    | ||      
TCCAGCTGTAGTTAGCAAATTATACAAGGCAATAAATTCCAATGGAGGTGTAACATATATACATTGCACTGCTGGACTTGGAAGAGCTCCAGCTGTTGCGgtatgtctcttggtttcttttatgtgatgcaagttactca---cagaatatt-tacctgaaatgttttgggttagatctaggtaaggtaaagga--aataatttcc

upper sequence: GRMZM2G052546_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv00s0250g00020.t01 (Vitis vinifera), 5'ss of exon 8
TCCTGCTGTGGTTAGCAAATTGCACAAACTTATCAACTGTAATGGTGGTGTAACATATATACATTGTACTGCTGGACTTGGAAGAGCTCCTGCTGTTGCAgtaggtttacatgccacccccccctaatttttgtttcccaagacaacttattgtttcacagattccttatgtttgtctagagatccttttgcttcagtag
||| |||||||| ||||||||  ||||    || ||  | ||||| ||||| || |||||||| || || ||||||||||| ||||||||||| || || ||| | ||           | |   ||| |   ||      | | |    || |  |  |||      |  | |   || |   |    | || | | | 
TCCAGCTGTGGTGAGCAAATTATACAAGGCGATAAATCGAAATGGAGGTGTGACTTATATACACTGCACAGCTGGACTTGGGAGAGCTCCTGCCGTGGCGgtatgcttctccattttgtctcagaaatatgaattaattctgcctaaggcttttagctaagaaatacgaattgtaattaaatggcacacttctacggaat

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|148952817|gb|EC898809.2|EC898809
EST:     TAACATATATACATTGTACTGCTGGACTTGGAAGAGCTCCTGCTGTTGCA                         TTGGCTTATATGTTCTGGATTCTTGGGTACAGTCTCAATGAAGGACATCGG
genomic: TAACATATATACATTGTACTGCTGGACTTGGAAGAGCTCCTGCTGTTGCAgtaggtttac ... aaaatttcagTTGGCTTATATGTTCTGGATTCTTGGGTACAGTCTCAATGAAGGACATCGG
EST: gi|148970824|gb|EE021591.2|EE021591
EST:     TAACATATATACATTGTACTGCTGGACTTGGAAGAGCTCCTGCTGTTGCA                         TTGGCTTATATGTTCTGGATTCTTGGGTACAGTCTCAATGAAGGACATCGG
genomic: TAACATATATACATTGTACTGCTGGACTTGGAAGAGCTCCTGCTGTTGCAgtaggtttac ... aaaatttcagTTGGCTTATATGTTCTGGATTCTTGGGTACAGTCTCAATGAAGGACATCGG
EST: gi|21621474|gb|BQ619480.1|BQ619480
EST:     TAACATATATACATTGTACTGCTGGACTTGGAAGAGCTCCTGCTGTTGCA                         TTGGCTTATATNGT-CTGGATTNCT-GGGTACAGTCTCAATGAAGGACATC
genomic: TAACATATATACATTGTACTGCTGGACTTGGAAGAGCTCCTGCTGTTGCAgtaggtttac ... aaaatttcagTTGGCTTATAT-GTTCTGGATT-CTTGGGTACAGTCTCAATGAAGGACATC
EST: gi|67023551|gb|CO452300.1|CO452300
EST:     TAACATATATACATTGTACTGCTGGACTTGGAAGAGCTCCTGCTGTTGCA                         TTGGCTTATATGTTCTGGATTCTTGGGTACAGTCTCAATGAAGGACATCGG
genomic: TAACATATATACATTGTACTGCTGGACTTGGAAGAGCTCCTGCTGTTGCAgtaggtttac ... aaaatttcagTTGGCTTATATGTTCTGGATTCTTGGGTACAGTCTCAATGAAGGACATCGG
EST: gi|71435430|gb|DR816480.1|DR816480
EST:     TAACATATATACATTGTACTGCTGGACTTGGAAGAGCTCCTGCTGTTGCA                         TTGGCTTATATGTTCTGGATTCTTGGGTACAGTCTCAATGAAGGACATCGG
genomic: TAACATATATACATTGTACTGCTGGACTTGGAAGAGCTCCTGCTGTTGCAgtaggtttac ... aaaatttcagTTGGCTTATATGTTCTGGATTCTTGGGTACAGTCTCAATGAAGGACATCGG
EST: gi|76290045|gb|DV029613.1|DV029613
EST:     TAACATATATACATTGTACTGCTGGACTTGNAAGAGCTCCTGCTGTTGCA                         TTGGCTTATATGTTCTGGATTCTTGGGTACAGTCTCAATGAAGGACATCGG
genomic: TAACATATATACATTGTACTGCTGGACTTGGAAGAGCTCCTGCTGTTGCAgtaggtttac ... aaaatttcagTTGGCTTATATGTTCTGGATTCTTGGGTACAGTCTCAATGAAGGACATCGG
EST: gi|74234762|gb|DT642676.1|DT642676
EST:     TAACATATATACATTGTACTGCTGGACTTGGAAGAGCTCCTGCTGTTGCA                         TTGGCTTATATGTTCTGGATTCTTGGGTACAGTCTCAATGAAGGACATCGG
genomic: TAACATATATACATTGTACTGCTGGACTTGGAAGAGCTCCTGCTGTTGCAgtaggtttac ... aaaatttcagTTGGCTTATATGTTCTGGATTCTTGGGTACAGTCTCAATGAAGGACATCGG
EST: gi|148967268|gb|EE018472.2|EE018472
EST:     TAACATATATACATTGTACTGCTGGACTTGGAAGAGCTCCTGCTGTTGCA                         TTGGCTTATATGTTCTGGATTCTTGGGTACAGTCTCAATGAAGGACATCGG
genomic: TAACATATATACATTGTACTGCTGGACTTGGAAGAGCTCCTGCTGTTGCAgtaggtttac ... aaaatttcagTTGGCTTATATGTTCTGGATTCTTGGGTACAGTCTCAATGAAGGACATCGG
EST: gi|148934585|gb|EC878634.2|EC878634
EST:     TAACATATATACATTGTACTGCTGGACTTGGAAGAGCTCCTGCTGTTGCA                         TTGGCTTATATGTTCT
genomic: TAACATATATACATTGTACTGCTGGACTTGGAAGAGCTCCTGCTGTTGCAgtaggtttac ... aaaatttcagTTGGCTTATATGTTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTGCTGTGGTTAGCAAATTGCACAAACTTATCAACTGTAATGGTGGTGTAACATATATACATTGTACTGCTGGACTTGGAAGAGCTCCTGCTGTTGCAgtaggtttacatgccacccccccctaatttttgtttcccaagacaacttattgtttcacagattccttatgtttgtctagagatccttttgcttcagtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT