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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taagcttccataatagacggtatggtcctactgatcagcatggaaactttgtcattgcaccacgcaaaactccaacgaacttctcatttgctgattacagGAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGCTTTCTTGCCAGAGGTGCAGAGCGCGGATAGGAAGATACCGTTCAGAGAA

Basic information

species Zea mays
transcript GRMZM2G073498_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073498_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 1
----taagcttccataatagacggtatggtcctactgatcagcatggaaactttgtcattgcaccacgcaaaactccaacgaacttctcatttgctgattacagGAA--GATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGCTTTCTTGCCAGAGGTGCAGAGCGCGGATAGGAAGATACCGTTCAGAGAA
    | | || |||   | ||   | |  | | |   |   |  |   || |||||   ||||     |||||     ||  | || |  ||   || | |||||||  ||||||||| ||||| |||||| ||||||| |||||||||||||| |||||| |||| || || ||||| || |||||||| ||||| || ||||  
agtctgaactaccaagtttgaaatttttttacaagacacatgttttataattttgtg--tgcattgtacaaaatcttgacctattttt--ttgcttggtcacagGAAAAGATGGCTGGTGGCTTTAGGGTATTGCATCTTGTCAGGCCTTTTCTGGCTTTCCTGCCTGAAGTACAGAGTGCTGATAGGAAAATACCATTTAGAG--
















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|211220854|gb|FL004691.1|FL004691
EST:     GGCGAMSSTTCTGTCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAG                         GAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTGGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAGgtaaatctgc ... ctgattacagGAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC
EST: gi|211220849|gb|FL004686.1|FL004686
EST:     GGCGAMSTTTCTGTCCTCCCNGGCGCCGGGCTCGGGTCGTCGTCGGCCAG                         GAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTRGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAGgtaaatctgc ... ctgattacagGAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC
EST: gi|211218780|gb|FL004672.1|FL004672
EST:     GGCGAAGCTTCTGTCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAG                         GAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTGGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAGgtaaatctgc ... ctgattacagGAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC
EST: gi|211220862|gb|FL004699.1|FL004699
EST:     GCGAACG-TTCTGTCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAG                         GAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTGGC
genomic: GCGAA-GCTTCTGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAGgtaaatctgc ... ctgattacagGAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC
EST: gi|211222924|gb|FL004709.1|FL004709
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAG                         GAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAGgtaaatctgc ... ctgattacagGAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC
EST: gi|211220863|gb|FL004700.1|FL004700
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAG                         GAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAGgtaaatctgc ... ctgattacagGAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC
EST: gi|211218786|gb|FL004678.1|FL004678
EST:     GCGAAS-TTCCTGTCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAG                         GAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTGGC
genomic: GCGAAGCTTC-TGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAGgtaaatctgc ... ctgattacagGAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC
EST: gi|211222921|gb|FL004706.1|FL004706
EST:     GCGAACG-TTCTGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAG                         GAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC
genomic: GCGAA-GCTTCTGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAGgtaaatctgc ... ctgattacagGAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC
EST: gi|211218789|gb|FL004681.1|FL004681
EST:     GGCGAAGCTTCTGTCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAG                         GAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTGGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAGgtaaatctgc ... ctgattacagGAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC
EST: gi|211218792|gb|FL004684.1|FL004684
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAG                         GAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAGgtaaatctgc ... ctgattacagGAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC
EST: gi|211220860|gb|FL004697.1|FL004697
EST:     GGCGAAGCTTCTGTCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAG                         GAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTGGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAGgtaaatctgc ... ctgattacagGAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC
EST: gi|78076684|gb|DV505118.1|DV505118
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAG                         GAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAGgtaaatctgc ... ctgattacagGAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC
EST: gi|211220857|gb|FL004694.1|FL004694
EST:     GGCGAAGCTTCTGTCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAG                         GAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTGGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAGgtaaatctgc ... ctgattacagGAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC
EST: gi|211218788|gb|FL004680.1|FL004680
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAG                         GAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAGgtaaatctgc ... ctgattacagGAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC
EST: gi|211220855|gb|FL004692.1|FL004692
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAG                         GAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAGgtaaatctgc ... ctgattacagGAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC
EST: gi|211454555|gb|FK953975.1|FK953975
EST:     CTGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAG                         GAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTGGC
genomic: CTGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAGgtaaatctgc ... ctgattacagGAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC
EST: gi|211220859|gb|FL004696.1|FL004696
EST:     GCGAACG-TTCTGCCCTCCCCGGMGCCGGGCTCGGGTCGTCGTCGGCCAG                         GAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC
genomic: GCGAA-GCTTCTGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAGgtaaatctgc ... ctgattacagGAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC
EST: gi|211220858|gb|FL004695.1|FL004695
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAG                         GAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAGgtaaatctgc ... ctgattacagGAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC
EST: gi|211222925|gb|FL004710.1|FL004710
EST:     GGCGAAGCTTCTGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAG                         GAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC
genomic: GGCGAAGCTTCTGCCCTCCCCGGCGCCGGGCTCGGGTCGTCGTCGGCCAGgtaaatctgc ... ctgattacagGAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actttgtcattgcaccacgcaaaactccaacgaacttctcatttgctgattacagGAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGCTTTCTTGCCAGAGGTGCAGAGCGCGGATAGGAAGATACCGTTCAGAGAA
                                           tgctgat  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taagcttccataatagacggtatggtcctactgatcagcatggaaactttgtcattgcaccacgcaaaactccaacgaacttctcatttgctgattacagGAAGATGGCTGGCGGCTTCAGGGTACTGCATCTGGTCAGGCCTTTTCTTGCTTTCTTGCCAGAGGTGCAGAGCGCGGATAGGAAGATACCGTTCAGAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- -gcttcca
- - - - - - - - - - - - - cctactg
- - - - - - - - - - - - - - - - - - -gcatgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -caccacg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caacgaa