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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATATGATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGAgtaagctctcttcattttttttaaaaaaaatatctgtgctggttgctgaaccagtgaaaaactatcctgaactgcatgtgctaattgcag

Basic information

species Zea mays
transcript GRMZM2G062425_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G062425_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g21830.1 (Oryza sativa), 5'ss of exon 4
TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATATGATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGAgtaag-----ctctcttcatttttt---ttaaaaaaaatatctgtg-ctggttgctgaaccagtgaaa-aactatcctgaactgcatgtgctaattgcag
 || ||  |||||||||  || || ||||| ||||||||||| || ||||||||| |||||||||| |||||||| || ||||| || |||||   || ||     || |||  ||| | |    | | || || || ||||  ||  |||  || |||||||| |||| | | ||  |  ||||||||| |||||
AGCATTCAAGCTTCCTGTTTCCCGCGTGATACACACTGTTGGGCCCATATATGATATGGACAAGCAACCTGAGGTCTCCTTAAATAATGCCTACACgttagtcgtcctttctaaattgtatagtattacaagaaaatttgtggttgcctgcaaaatcagtgaaataactgttccga--ttgatgtgctaactgcag
















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|211309014|gb|FL381286.1|FL381286
EST:     ATATATGATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGA                         AAATAGCTTGAAGCTTGCTAAAGATAATGGCATTCAGTACATCGC
genomic: ATATATGATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGAgtaagctctc ... ctaattgcagAAATAGCTTGAAGCTTGCTAAGGATAATGGCATTCAGTACATCGC
EST: gi|211493989|gb|FL180888.1|FL180888
EST:     ATATATGATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGA                         AAATAGCTTGAAGCTTGCTA-GGATAATGGCAT-CAGTACATCGC
genomic: ATATATGATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGAgtaagctctc ... ctaattgcagAAATAGCTTGAAGCTTGCTAAGGATAATGGCATTCAGTACATCGC
EST: gi|211066115|gb|FL180931.1|FL180931
EST:     ATATATGATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGA                         AAATAGCTTGAAGCTTGCTAAAAGATAATGGCATTCAGTTACATCGCATTC
genomic: ATATATGATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGAgtaagctctc ... ctaattgcagAAATAGCTTGAAGCTTGCTAAG-GATAATGGCATTCAGT-ACATCGCATTC
EST: gi|211312231|gb|FK994146.1|FK994146
EST:     ATATATGATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGA                         AAATAGCTTGAAGCTTGCTAA
genomic: ATATATGATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGAgtaagctctc ... ctaattgcagAAATAGCTTGAAGCTTGCTAA
EST: gi|211214235|gb|FL024779.1|FL024779
EST:     ATATATGATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGA                         AAATAGCTTGAAGCTTGCTAAAGATAATGGCATTCAGTACATCGCGTTCCC
genomic: ATATATGATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGAgtaagctctc ... ctaattgcagAAATAGCTTGAAGCTTGCTAAGGATAATGGCATTCAGTACATCGCATTCCC
EST: gi|211066121|gb|FL180937.1|FL180937
EST:     ATATATGATTTG-ACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGA                         AAATAGCTTGAAGCTTGCTAAAGATAATGGCATTCAGTACATCGCATT
genomic: ATATATGATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGAgtaagctctc ... ctaattgcagAAATAGCTTGAAGCTTGCTAAGGATAATGGCATTCAGTACATCGCATT
EST: gi|211350576|gb|FL379662.1|FL379662
EST:     TATATTGATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGA                         AAATAGCTTGAAGCTTGCTAAGGATAATGGCATTCA
genomic: TATAT-GATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGAgtaagctctc ... ctaattgcagAAATAGCTTGAAGCTTGCTAAGGATAATGGCATTCA
EST: gi|211493995|gb|FL180894.1|FL180894
EST:     ATATATGATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGA                         AAATAGCTTGAAGCTTGCTAAAGATAATGGCATTCAGTACATC
genomic: ATATATGATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGAgtaagctctc ... ctaattgcagAAATAGCTTGAAGCTTGCTAAGGATAATGGCATTCAGTACATC
EST: gi|211214236|gb|FL024780.1|FL024780
EST:     ATATATGATTTGGACAAGCATCCTGAGGTGTCATTAGAGAAGGCCTATGA                         AAATAGCTTGAAGCTTGCTAAAGATAATGGCATTCAGTACATCGCATTCCC
genomic: ATATATGATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGAgtaagctctc ... ctaattgcagAAATAGCTTGAAGCTTGCTAAGGATAATGGCATTCAGTACATCGCATTCCC
EST: gi|20208314|gb|BQ134403.1|BQ134403
EST:     ATATATGATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGA                         AAATAGCTTGAAGCTTGCTAAAGATAATGGCATTCAGTACATCGCATTCCC
genomic: ATATATGATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGAgtaagctctc ... ctaattgcagAAATAGCTTGAAGCTTGCTAAGGATAATGGCATTCAGTACATCGCATTCCC
EST: gi|211207798|gb|FL424436.1|FL424436
EST:     ATATATGATTTGGACAATCATCCTGAGGTGTCATTAAAGAAGGCCTATGA                         AAATAGCTTGAAGCTT
genomic: ATATATGATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGAgtaagctctc ... ctaattgcagAAATAGCTTGAAGCTT
EST: gi|211494000|gb|FL180899.1|FL180899
EST:     ATATATGATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGA                         AAATAGCTTGAAGCTTGCTAAAGATAATGGCATTCAGTACATCGCATTCCC
genomic: ATATATGATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGAgtaagctctc ... ctaattgcagAAATAGCTTGAAGCTTGCTAAGGATAATGGCATTCAGTACATCGCATTCCC
EST: gi|211034222|gb|FL370386.1|FL370386
EST:     ATATATGATTTGGACAATCATCCTGAGGTGTCATTAAAGAAGGCCTATGA                         AAATAGCTTGAAGCTTGCTAAAGATAATGGCATTCAGTACATCGCATTTCC
genomic: ATATATGATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGAgtaagctctc ... ctaattgcagAAATAGCTTGAAGCTTGCTAAGGATAATGGCATTCAGTACATCGCATT-CC
EST: gi|20803361|gb|BQ294411.1|BQ294411
EST:     ATATATGATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGA                         AAATAGCTTGAAGCTTGCTAAAGATAATGGCATTCAGTACATCGCATTCCC
genomic: ATATATGATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGAgtaagctctc ... ctaattgcagAAATAGCTTGAAGCTTGCTAAGGATAATGGCATTCAGTACATCGCATTCCC
EST: gi|211329865|gb|FL380475.1|FL380475
EST:     ATATATGATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGA                         AAATAGCTTGAAGCTTGCTAAGGATAATGGCATTCAGTACATCGCATTCCC
genomic: ATATATGATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGAgtaagctctc ... ctaattgcagAAATAGCTTGAAGCTTGCTAAGGATAATGGCATTCAGTACATCGCATTCCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTTTTGAGCTTCCTGCCTCTCGGGTGATTCACACTGTTGGCCCTATATATGATTTGGACAAGCATCCTGAGGTGTCATTAAAGAAGGCCTATGAgtaagctctcttcattttttttaaaaaaaatatctgtgctggttgctgaaccagtgaaaaactatcctgaactgcatgtgctaattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG