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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttgttagcacattaagtacaatgttctgttgttgtctatgcttttggttctccgcagtaacatggttaccctcctgatattctgaagGCAAAGCTAGGGGAACAGAACAAGTTCTACTATGACGAGAAGCTGAAGCGGTGGGTTGAAGAAGGTGCTGAGATCCCTGCCGAGGAGCCCCCACTTCCCC

Basic information

species Zea mays
transcript GRMZM2G104958_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104958_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os06g01650.1 (Oryza sativa), 3'ss of exon 11
gtacttgttagcacattaagtacaat--gttctgttgttg---tctatgcttt--tggttctccgca---gtaacatggttaccctcctgatattctgaagGCAAAGCTAGGGGAACAGAACAAGTTCTACTATGACGAGAAGCTGAAGCGGTGGGTTGAAGAAGGTGCTGAGATCCCTGCCGAGGAGCCCCCACTTCCCC
|| |||| ||  ||||||| | ||     | | | | | |   |  |||      | ||| |        ||||||    ||      |  |   || ||||| ||||| |||||||| |||||||||||||||||||||||||||||||||||||| |||||||||||||| || ||||| |||||||| || |||||||
gtgcttgctaaaacattaaattcatccgatcccggtttcgaactgcatgtcacagtagtttttgatttgtgtaacacaactaattcttttgtgccctaaagGCGAAGCTGGGGGAACAAAACAAGTTCTACTATGACGAGAAGCTGAAGCGGTGGGTGGAAGAAGGTGCTGACATACCTGCTGAGGAGCCTCCCCTTCCCC

upper sequence: GRMZM2G104958_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA01G41800.1 (Glycine max), 3'ss of exon 13
gtacttgttagcacattaagtacaatgttctgttgttgtctatgcttttggttctccgcagtaacatggttaccc-tcctgatat-tctgaagGCAAAGCTAGGGGAACAGAACAAGTTCTACTATGACGAGAAGCTGAAGCGGTGGGTTGAAGAAGGTGCTGAGATCCCTGCCGAGGAGCCCCCACTTCCCC
|||    | |     |||  | |    || | ||     |  ||||| ||  | | |   || | |||||||    | ||  | | | || |||| ||  | || ||  | ||||||||||| ||||| |||||||||||| | ||||| ||||||||||||||  | || || || ||  |  |   ||  |
gtataattaattgttttattttc---tttttattcacaacagtgcttctgactgtgcatggtcaaatggttatttattctactctatatgtagGCTAAATTGGGTGAGAAAAACAAGTTCTATTATGATGAGAAGCTGAAGAGATGGGTGGAAGAAGGTGCTGAACTTCCAGCTGAAGAAGCTGCTGCTCTGC

upper sequence: GRMZM2G104958_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA11G03580.1 (Glycine max), 3'ss of exon 16
gtacttgttagcacattaagtacaatgttctgttgttgtctatgcttttggttctccgcagtaacatggttaccctcctg-atattctgaagGCAAAGCTAGGGGAACAGAACAAGTTCTACTATGACGAGAAGCTGAAGCGGTGGGTTGAAGAAGGTGCTGAGATCCCTGCCGAGGAGCCCCCACTTCCCC
||| |  ||||    || | |      || | ||     |  ||||| ||  | | |    | | ||||||    | ||  |   | || |||| ||  | || ||  | || |||||||| ||||| |||||||||||| | ||||| || |||||||||||  | || || || ||  |  |   ||   
gta-taattagttgttttatttt--ctttttattcacaacagtgcttctgactgtgcctgttcaaatggttcttgttctacactatatgtagGCTAAATTGGGTGACAAAAATAAGTTCTATTATGATGAGAAGCTGAAGAGATGGGTGGAGGAAGGTGCTGAAGTTCCAGCTGAAGAAGCTGCTGCTCTGA

upper sequence: GRMZM2G104958_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA11G03590.1 (Glycine max), 3'ss of exon 17
gtacttgttagcacattaagtacaatgttctgttgttgtctatgcttttggttctccgcagtaacatggttaccctcctgatat-tctgaagGCAAAGCTAGGGGAACAGAACAAGTTCTACTATGACGAGAAGCTGAAGCGGTGGGTTGAAGAAGGTGCTGAGATCCCTGCCGAGGAGCCCCCACTTCCCC
||| |  ||||    || | |      || | ||     |  ||||| || || | |    | | ||||||    | ||  | | | || |||| ||  | || ||  | ||||||||||| ||||| |||||||||||| | ||||| || |||||||||||  | || || || ||  |  |   ||  |
gta-taattagttgttttatttt--ctttttattcaccacagtgcttctgattgtgcctgtttaaatggttcttattctactctatatgtagGCTAAATTGGGTGAGAAAAACAAGTTCTATTATGATGAGAAGCTGAAGAGATGGGTGGAGGAAGGTGCTGAAGTTCCAGCTGAAGAAGCTTCTGCTCTGC

upper sequence: GRMZM2G104958_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA01G41790.1 (Glycine max), 3'ss of exon 15
gtacttgttagcacattaagtacaatgttctgttgttgtctatgcttttggttctccgcagtaacatggttaccctcctgatat---tctgaagGCAAAGCTAGGGGAACAGAACAAGTTCTACTATGACGAGAAGCTGAAGCGGTGGGTTGAAGAAGGTGCTGAGATCCCTGCCGAGGAGCCCCCACTTCCCC
||| |  ||||    || | |      || | ||     |  ||||| || || | |    | |  |||||    | ||  | |   | || |||| ||  | || ||  | ||||||||||| ||||| |||||||||||  | ||||| || |||||||||||  | || || || ||  |  |   ||  |
gta-taattagttgttttatttt--ctttatattcacaacagtgcttctgattgtgcctgtttaagtggttcttattctactctgtatatgtagGCTAAATTGGGTGAGAAAAACAAGTTCTATTATGATGAGAAGCTGAAAAGATGGGTGGAGGAAGGTGCTGAACTTCCAGCTGAAGAAGCTGCTGCTCTGC

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|31361599|gb|CD445956.1|CD445956
EST:     GATGGTTGGTGCAGAAGACAATAGGGCTTGTTTCAAAATCTCACCGCCAG                         GCAAAGCTAGGGGAACAGAACAAGTTCTACTATGACGA
genomic: GATGGTTGGTGCAGAAGACAATAGGGCTTGTTTCAAAATCTCACCGCCAGgtacttgtta ... tattctgaagGCAAAGCTAGGGGAACAGAACAAGTTCTACTATGACGA
EST: gi|67040032|gb|CO466287.1|CO466287
EST:     GATGGTTGGTGCAGAAGACAATGGGGCTTGTTTCAAAATCTCACCGCCAG                         GCAAAGCTAGGGGAACAGAACAAGTTCTACTATGACGAGAAGCTGAAGCGG
genomic: GATGGTTGGTGCAGAAGACAATAGGGCTTGTTTCAAAATCTCACCGCCAGgtacttgtta ... tattctgaagGCAAAGCTAGGGGAACAGAACAAGTTCTACTATGACGAGAAGCTGAAGCGG
EST: gi|32832663|gb|CD972341.1|CD972341
EST:     GATGGTTGGTGCAGAAGACAATAGGGCTTGTTTCAAAATCTCACCGCCAG                         GCAAAGCTAGGGGAACAGAACAAGTTCTACTATGACGAGAAGCTGAAGCGG
genomic: GATGGTTGGTGCAGAAGACAATAGGGCTTGTTTCAAAATCTCACCGCCAGgtacttgtta ... tattctgaagGCAAAGCTAGGGGAACAGAACAAGTTCTACTATGACGAGAAGCTGAAGCGG
EST: gi|71312083|gb|DR792565.1|DR792565
EST:     GATGGTTGGTGCAGAAGACAATAGGGCTTGTTTCAAAATCTCACCGCCAG                         GCAAAGCTAGGGGAACAGAACAAGTTCTACTATGACGAGAAGCTGAAGCGG
genomic: GATGGTTGGTGCAGAAGACAATAGGGCTTGTTTCAAAATCTCACCGCCAGgtacttgtta ... tattctgaagGCAAAGCTAGGGGAACAGAACAAGTTCTACTATGACGAGAAGCTGAAGCGG
EST: gi|71448602|gb|DR829652.1|DR829652
EST:     GATGGTTGGTGCAGAAGACAATAGGGCTTGTTTCAAAATCTCACCGCCAG                         GCAAAGCTAGGGGAACAGAACAAGTTCTACTATGACGAGAAGCTGAAGCGG
genomic: GATGGTTGGTGCAGAAGACAATAGGGCTTGTTTCAAAATCTCACCGCCAGgtacttgtta ... tattctgaagGCAAAGCTAGGGGAACAGAACAAGTTCTACTATGACGAGAAGCTGAAGCGG
EST: gi|32919484|gb|CF024296.1|CF024296
EST:     GATGGTTGGTGCAGAAGACAATAGGGCTTGTTTCAAAATCTCACCGCCAG                         GCAAAGCTAGGGGAACAGAACAAGTTCTACTATGACGAGAAGCTGAAGCGG
genomic: GATGGTTGGTGCAGAAGACAATAGGGCTTGTTTCAAAATCTCACCGCCAGgtacttgtta ... tattctgaagGCAAAGCTAGGGGAACAGAACAAGTTCTACTATGACGAGAAGCTGAAGCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtctatgcttttggttctccgcagtaacatggttaccctcctgatattctgaagGCAAAGCTAGGGGAACAGAACAAGTTCTACTATGACGAGAAGCTGAAGCGGTGGGTTGAAGAAGGTGCTGAGATCCCTGCCGAGGAGCCCCCACTTCCCC
                                          tgatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttgttagcacattaagtacaatgttctgttgttgtctatgcttttggttctccgcagtaacatggttaccctcctgatattctgaagGCAAAGCTAGGGGAACAGAACAAGTTCTACTATGACGAGAAGCTGAAGCGGTGGGTTGAAGAAGGTGCTGAGATCCCTGCCGAGGAGCCCCCACTTCCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG