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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcataacgtttactctattttgttcataacgtttactctattttgtgcatgatattctttttttggtaacatgttcctttgttgatgttctgttttccagCCTACAACAGAGTGACGAGACTCCAATGGTCTGGGAGATCCTTCTTTATATGTATGTCCTTTATTCGCCGGACTGGCATTACAGGAGCACAATGCCAACC

Basic information

species Zea mays
transcript GRMZM2G300944_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G300944_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g49180.1 (Oryza sativa), 3'ss of exon 2
-tcataacgtttactctattttgttcataacgtttactctattttgtgcatgatattctttttttggtaacatgttcctttgttgatgttctgttttccagCCTACAACAGAGTGACGAGACTCCAATGGTCTGGGAGATCCTTCTTTATATGTATGTCCTTTATTCGCCGGACTGGCATTACAGGAGCACAATGCCAACC
| || | | | || || | || | ||| | || | | | || | ||| |||| | |||| |||||||||| |||| ||||| || |||||||||||||| |||||||| || || ||| | ||||| |||||||| || |||||||||||| ||||||| ||||| ||
ctaattgggggcagctagtattcatcttctaattccagcatgtttccttagtatgcacaatatgcagtgcta-attcttttggtcatgtattgttttccagTTTACAGCAGAGCGATGAGACTCCAATGGTGTGGGAGATTCTCCTATATCTTTATGTACTTTATTCACCAGACTGGCATTACCGGAGCACTATGCCTACT

upper sequence: GRMZM2G300944_T03 (Zea mays), 3'ss of exon 2
lower sequence: AT4G22330.1 (Arabidopsis thaliana), 3'ss of exon 2
tcataacgtttactctattttgttcataacgtttactctattttgtgcatgatattctttttttggtaacatgttcct-ttgttgatgttctgttttc---cagCCTACAACAGAGTGACGAGACTCCAATGGTCTGGGAGATCCTTCTTTATATGTATGTCCTTTATTCGCCGGACTGGCATTACAGGAGCACAATGCCAACC
||| | | | || | |||| || | | |||| | |||||| | | | | || | | | | | || |||| ||| | |||||||||||| ||||| |||||||| |||||||| ||||| || ||||| ||||||| || || || ||||||||| | || |||||||| ||
--atatgtagttgtttgattgatgcatagaactt--ttcaaattgttattagtattctggtctaaatttcggattaaaactctcggtttcttgatttcaatcagGCAACAACAGAGTGATGAGACCCCAATGGTGTGGGAGATACTTCTATACATGTACATCCTTTACTCACCAGATTGGCATTACCGAAGTACAATGCCCACT

upper sequence: GRMZM2G300944_T03 (Zea mays), 3'ss of exon 2
lower sequence: PP1S55_117V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------------------------------tcataacgtttactc-tattttgttcataacgtttac----tctattttgtgca-tgatattctttttttggtaacatgttcctttgttgatgttctgttttc---cagCCTACAACAGAGTGACGAGACTCCAATGGTCTGGGAGATCCTTCTTTATATGTATGTCCTTTATTCGCCGGACTGGCATTACAGGAGCACAATGCCAACC
|||| || || | ||||| || ||| | ||| | | | || | | || | || || | || |||| | |||| | ||| | ||| |||||||| |||||||| ||||| |||| ||| ||||| || || || || |||||||| || |||||||| || ||||||||||||| ||
gtaagctttttacactttacttttaacagtgctcatatacatcttactcgtccatgcctgtgcttaatgtggacatgcatatcgaatatcgatgttttgactg-aatatttggaagatatataccctcaagttgtagtgtcttactagttac-tttttttttgcatgcgcgacgtttgcgagcagTCAACAGCAGAGTGATGAGACTCCTATGGTATGGGTGATGCTTCTCTACATCTACGTGCTTTATTCTCCAGACTGGCACTATCGGAGCACAATGCCCACA

upper sequence: GRMZM2G300944_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ18347 (Selaginella moellendorffii), 3'ss of exon 1
tcataacgtttactctattttgttcataacgtttactctattttgtgcatgatattctttttttggtaacatgttcc---tttgttgatgttctgttttccagCCTACAACAGAGTGACGAGACTCCAATGGTCTGGGAGATCCTTCTTTATATGTATGTCCTTTATTCGCCGGACTGGCATTACAGGAGCACAATGCCAACC
| || | ||| ||| || ||| | | | | | | | | |||| | |||||| || | || | | |||||| | ||| ||||| |||||||||||||||||||||| ||| || || || || || || || || || ||||||||||| ||| | ||||||||||| ||
ttatca-gttcttcctaagccaagttctactcctacgatctctaggactt--tttggttttcagatctatatgttctaagttccaaaactttttttcttccagGCAACAGCAGAGCGACGAGACTCCAATGGTCTGGGTGATGCTCCTCTACATCTACGTGCTCTACTCCCCGGACTGGCACTACCGCAGCACAATGCCGACG

upper sequence: GRMZM2G300944_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ22064 (Selaginella moellendorffii), 3'ss of exon 1
tcataacgtttactctattttgttcataacgtttactctattttgtgcatgatattctttttttggtaacatgttcc---tttgttgatgttctgttttccagCCTACAACAGAGTGACGAGACTCCAATGGTCTGGGAGATCCTTCTTTATATGTATGTCCTTTATTCGCCGGACTGGCATTACAGGAGCACAATGCCAACC
| || | ||| ||| || ||| | | | | | | | |||| | |||||| || | || | | |||||| | ||| ||||| |||||||||||||||||||||| ||| || || || || || || || || || ||||||||||| ||| | ||||| ||||| ||
ttatca-gttcttcctaagccaagttctactcctacgatctctaagactt--tttggttttcagatctatatgttctaagttccaaaactttttctcttccagGCAACAGCAGAGCGACGAGACTCCAATGGTCTGGGTGATGCTCCTCTACATCTACGTGCTCTACTCCCCGGACTGGCACTACCGCAGCACGATGCCGACG

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|148965554|gb|EE016382.2|EE016382
EST:     ATGATACTTGCTATTGGGAGTATGATTTTTCATGCCACCTTGCAACTTGT                         CCTACAACAGAGTGACGAGACTCCAATGGTCTGGGAGATCCTTCTTTATAT
genomic: ATGATACTTGCTATTGGGAGTATGATTTTTCATGCCACCTTGCAACTTGTgtaagtttcc ... tgttttccagCCTACAACAGAGTGACGAGACTCCAATGGTCTGGGAGATCCTTCTTTATAT
EST: gi|78108960|gb|DV527377.1|DV527377
EST:     ATGATACTTGCTATTGGGAGTATGATTTTTCATGCCACCTTGCAACTTGT                         CCTACAACAGAGTGACGAGACTCCAATGGTCTGGGAGATCCTTCTTTATAT
genomic: ATGATACTTGCTATTGGGAGTATGATTTTTCATGCCACCTTGCAACTTGTgtaagtttcc ... tgttttccagCCTACAACAGAGTGACGAGACTCCAATGGTCTGGGAGATCCTTCTTTATAT
EST: gi|74245190|gb|DT653104.1|DT653104
EST:     ATGATACTTGCTATTGGGAGTATGATTTTTCATGCCACCTTGCAACTTGT                         CCTACAACAGAGTGACGAGACTCCAATGGTCTGGGAGATCCTTCTTTATAT
genomic: ATGATACTTGCTATTGGGAGTATGATTTTTCATGCCACCTTGCAACTTGTgtaagtttcc ... tgttttccagCCTACAACAGAGTGACGAGACTCCAATGGTCTGGGAGATCCTTCTTTATAT
EST: gi|211393645|gb|FL322584.1|FL322584
EST:     ATGATACTTGCTATTGGGAGTATGATTTTTCATGCCACCTTGCAACTTGT                         CCTACAACAGAGTGACGAGACTCCAATGGTCTGGGAGATCCTTCTTTATAT
genomic: ATGATACTTGCTATTGGGAGTATGATTTTTCATGCCACCTTGCAACTTGTgtaagtttcc ... tgttttccagCCTACAACAGAGTGACGAGACTCCAATGGTCTGGGAGATCCTTCTTTATAT
EST: gi|71445861|gb|DR826911.1|DR826911
EST:     ATGATACTTGCTATTGGGAGTATGATTTTTCATGCCACCTTGCAACTTGT                         CCTACAACAGAGTGACGAGACTCCAATGGTCTGGGAGATCCTTCTTTATAT
genomic: ATGATACTTGCTATTGGGAGTATGATTTTTCATGCCACCTTGCAACTTGTgtaagtttcc ... tgttttccagCCTACAACAGAGTGACGAGACTCCAATGGTCTGGGAGATCCTTCTTTATAT
EST: gi|91877863|gb|EB407820.1|EB407820
EST:     ATGATACTTGCTATTGGGAGTATGATTTTTCATGCCACCTTGCAACTTGT                         CCTACAACAGAGTGACGAGACTCCAATGGTCTGGGAGATCCTTCTTTATAT
genomic: ATGATACTTGCTATTGGGAGTATGATTTTTCATGCCACCTTGCAACTTGTgtaagtttcc ... tgttttccagCCTACAACAGAGTGACGAGACTCCAATGGTCTGGGAGATCCTTCTTTATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatgatattctttttttggtaacatgttcctttgttgatgttctgttttccagCCTACAACAGAGTGACGAGACTCCAATGGTCTGGGAGATCCTTCTTTATATGTATGTCCTTTATTCGCCGGACTGGCATTACAGGAGCACAATGCCAACC
                                          ttctgttttcc  CT-rich tract
 atattcttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcataacgtttactctattttgttcataacgtttactctattttgtgcatgatattctttttttggtaacatgttcctttgttgatgttctgttttccagCCTACAACAGAGTGACGAGACTCCAATGGTCTGGGAGATCCTTCTTTATATGTATGTCCTTTATTCGCCGGACTGGCATTACAGGAGCACAATGCCAACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - -ttttgtt
- - - - - - - - - - - - - - - - - - - - - - -tgcatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgat