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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagacaaagttatattgcatagtcaatccatgttttgtcgtcttggtcaccgtaaatagactagggtttctttagttctattaggatctaagtgcttattctctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGTAAACATTGATATATCAGTTG

Basic information

species Zea mays
transcript GRMZM2G044237_T03
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044237_T03 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os03g17120.1 (Oryza sativa), 3'ss of exon 14
gttagacaaagttatattgcatagtcaatccatgttttgtcgtcttggtcaccgtaaatagactagggtttctttagttct---attaggatctaag-tgcttattctctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGTAAACATTGATATATCAGTTG
||||   ||  ||  |   |||||  |||   | ||||    | |||   ||  | |||  | |    ||| | ||| |||   | ||| || |||  |   || | | | |   |||||   | || ||||||||||| ||||||||||||||   |||||||||||| ||||||||| |||||||||
gttaagaaaccttg-acaacatag--aattattttttt----tattgacgactttgaatgaattgtaatttgtgtagatcttacaatagaatttaaaatatctactgtttcttcatagATCTGCGGCCAGCAAGTATCTGAAAGATGCTGGAGACATCCATGGTACAGTGAACATTGATGTATCAGTTG
















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|74242072|gb|DT649986.1|DT649986
EST:     CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAG                         ATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT
genomic: CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAGgttagacaaa ... ctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT
EST: gi|32934567|gb|CF039379.1|CF039379
EST:     CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAG                         ATTGGCCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGT
genomic: CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAGgttagacaaa ... ctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGT
EST: gi|32835096|gb|CD974774.1|CD974774
EST:     CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAG                         ATTGGCCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTA
genomic: CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAGgttagacaaa ... ctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTA
EST: gi|149009105|gb|EE153803.2|EE153803
EST:     TGAAAAATGGGCAACCACTCCCCTTTGACAG                         ATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT
genomic: TGAAAAATGGGCAACCACTCCCCTTTGACAGgttagacaaa ... ctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT
EST: gi|78092274|gb|DV520648.1|DV520648
EST:     CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAG                         ATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT
genomic: CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAGgttagacaaa ... ctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT
EST: gi|148972814|gb|EE023800.2|EE023800
EST:     CTGGGAGTTATTTCACTAATGAAAAAGGGGCAACCACTCCCCTTTGACAG                         ATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT
genomic: CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAGgttagacaaa ... ctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT
EST: gi|60349194|gb|DN216167.1|DN216167
EST:     GGGCAACCACTCCCCTTTGACAG                         ATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT
genomic: GGGCAACCACTCCCCTTTGACAGgttagacaaa ... ctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT
EST: gi|148938789|gb|EC883127.2|EC883127
EST:     CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAG                         ATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT
genomic: CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAGgttagacaaa ... ctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT
EST: gi|32928445|gb|CF033257.1|CF033257
EST:     CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAG                         ATTGGCCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGT
genomic: CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAGgttagacaaa ... ctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGT
EST: gi|76917242|gb|DV166726.1|DV166726
EST:     CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAG                         ATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT
genomic: CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAGgttagacaaa ... ctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT
EST: gi|211349360|gb|FL434476.1|FL434476
EST:     CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAG                         ATTGGCCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT
genomic: CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAGgttagacaaa ... ctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT
EST: gi|78027443|gb|DV495830.1|DV495830
EST:     CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAG                         ATTGGCCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT
genomic: CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAGgttagacaaa ... ctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agactagggtttctttagttctattaggatctaagtgcttattctctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGTAAACATTGATATATCAGTTG
                                   tgcttattctctttct  CT-rich tract
         tttcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagacaaagttatattgcatagtcaatccatgttttgtcgtcttggtcaccgtaaatagactagggtttctttagttctattaggatctaagtgcttattctctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGTAAACATTGATATATCAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG