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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttccgctttcccgggccgatctctcggcggcgacctagctgctggacagatcgagatctgaaaaaatggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC

Basic information

species Zea mays
transcript GRMZM2G127948_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G127948_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g06980.2 (Oryza sativa), 3'ss of exon 2
gtatgttccgctttcccgggccgatctctcgg-cggcgacctagctgctggacagatcga--------gatctgaaaaaatgg--------cgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC
||| | || | ||| | |||| || | ||| | || | ||||| ||| | | || | | |||||||||||||||||||| || || ||||||||||| ||||||||| |||| | ||||||||||||||||||||||||||||||||||||||||||||||||
gtacgccacgaatcccctcctcctcctcttgggccccgaatcggagctcggcgacatcgatttgattcgattgggagggatcgatgttgttcttgcagGAACCTGATGACGACGTCGGCGGACGAGGGGCAATTCCTGAACCTGCTGCTGAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC

upper sequence: GRMZM2G127948_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G33780.1 (Glycine max), 3'ss of exon 2
------------------------------------gtatgttccgctttcccgggccgatctctcggcggcgacctagctgctgg--acagatcgagatctgaaaaaatggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC
|| || | ||| | || | ||| ||| || ||| |||||||| | ||||||| | ||||| ||||| || ||||| ||||||||| ||||||||||| | ||||||||| |||||||| |||||||| || || |||||||| ||
gtatatataatttatataatttcattttttcaattgacattttgacacctattaatatgattggtt--tggtttctctgctcgtggttactgattttttgttgaaaaaaaaaca-acagGAACATCATGACAACCTCTGCAGACGAAGGGCAGTTCTTGAACATGCTCCTTAAGCTCATCAATGCCAAGAACACCATGGAAATTGGTGTCTACACTGGG

upper sequence: GRMZM2G127948_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G11530.1 (Glycine max), 3'ss of exon 2
-----------------------------gtatgttccgctttcccgggccgatctctcggcggcgacctagctgctgg--acagatcgagatctgaaaaaatggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC
| || | | | || || | ||| ||| || ||| | |||| ||||||| | ||||| ||||| || ||||| ||||| ||| ||||||||||| | ||||||||| |||||||| |||||||| || || |||||||| ||
gtatatatataactatttcatttttcaattgacattttgactcctatttatatgcttcgtttggtttctctgctcatggttactgattttttttgttgaaaacaaacaacagGAACATCATGACAACCTCTGCAGACGAAGGGCAATTCTTGAACATGCTCCTTAAGCTCATCAATGCCAAGAACACCATGGAAATTGGTGTCTACACTGGA

upper sequence: GRMZM2G127948_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv03s0063g00140.t01 (Vitis vinifera), 3'ss of exon 2
---------gtatgttccgctttcccgggcc---gatctctcggcggcgacctagc---tgctggacagatcgagatctgaaaaaatggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC
|| | || ||| | | || | || | | | | || | | | | | | || ||||||| | ||||| || || || || || ||||||||| |||||||||| ||||||||||| |||||||| ||||||||||| ||||||||||| |||
gtgagcttttcttgattcggattctcaaatctttgaatacccgttgtctatttgatgcttgtttgtaacgttagtgttggtttgaaaacgaaacagGAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCTCAAGCTCATCAATGCCAAGAACACCATGGAGATAGGCGTCTACACTGGC

upper sequence: GRMZM2G127948_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv07s0031g00350.t01 (Vitis vinifera), 3'ss of exon 2
-----------gtatgttccgctttcccgggccgatctctcggcggc-------gaccta---gctgctggacagatcgagatctgaaaa--aatggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC
| | | | || | | || || || || | | | || ||| | | | | || |||| | ||||||| | ||||||||||| || || || ||||||||| |||||||||| |||| |||||| ||||||||| |||||||| |||||||| |||||||||
gtgagagatgagattcattcaacctctgtgtctgaattcatactggattaatgggatcaataggatgatggttttaatggagcttaagaattaatgatg-acagGAACATCATGACGACCTCGGCTGATGAAGGGCAGTTCTTGAACATGCTGCTCAAACTCATCAACGCCAAGAACACCATGGAAATCGGCGTTTACACCGGC

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|50324343|gb|CO519469.1|CO519469
EST:     GAGCCGGAGAGCATGAAGGAGCTCCGCGAGATCACCGCCAAGCACCCATG                         GAACCTGATGACGACCTCCGCCGACGATTTTTAGTTCCTGAACATGCTCAT
genomic: GAGCCGGAGAGCATGAAGGAGCTCCGCGAGATCACCGCCAAGCACCCATGgtatgttccg ... tggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCAT
EST: gi|29544906|gb|CB605514.1|CB605514
EST:     AGCCGGAGATGT-TGTAGGAGCTCCGCGAGATCACCGCCAAGCACCCATG                         GAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCAT
genomic: AGCCGGAGA-GCATGAAGGAGCTCCGCGAGATCACCGCCAAGCACCCATGgtatgttccg ... tggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCAT
EST: gi|9952456|gb|BE639039.1|BE639039
EST:     GAGCCGGAGAGCATGAAGGAGCTCCGCGAGATCACCGCCAAGCACCCATG                         GAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCAT
genomic: GAGCCGGAGAGCATGAAGGAGCTCCGCGAGATCACCGCCAAGCACCCATGgtatgttccg ... tggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcggcggcgacctagctgctggacagatcgagatctgaaaaaatggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC
                                     tgaaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttccgctttcccgggccgatctctcggcggcgacctagctgctggacagatcgagatctgaaaaaatggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC