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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcaatatgcttcatgcttgcaaaactgtagttcttattctaatgaactgctggtttctgatggcattttgttttcatgttacagTCTGATCCTCGTGTTAAAGAGAAGGTATTGGTGCTGATAGATACATGGCAAGACGTGTTTGGGGGATCACATGCAAGATATCCACAATACTATGCAGCAT

Basic information

species Zea mays
transcript GRMZM2G062953_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G062953_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g12880.1 (Oryza sativa), 3'ss of exon 3
gttcaatatgcttcatgcttgcaaaactgtagt-tcttattctaatgaactgctggtttctgatggcattt--tgttttcatgttacagTCTGATCCTCGTGTTAAAGAGAAGGTATTGGTGCTGATAGATACATGGCAAGACGTGTTTGGGGGATCACATGCAAGATATCCACAATACTATGCAGCAT
|||  ||||||| |||  ||   |        | | || || |||||  |||      | ||||||||| |  | || || | |||||||||||||    ||| ||||||||||||||     ||||||||||||||||||| |  || |||||| ||| ||||||||||||||| ||||||||||| |
gtttgatatgctccatagttttgatctcaagctgttttgttttaatgtcctgaa----tatgatggcatatgttcttgtcctattacagTCTGATCAGAATGTCAAAGAGAAGGTATTAACTATGATAGATACATGGCAAGAAGCATTCGGGGGACCACGTGCAAGATATCCACAGTACTATGCAGCGT

upper sequence: GRMZM2G062953_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT4G32760.1 (Arabidopsis thaliana), 3'ss of exon 3
gttcaatatgcttcatgcttgcaaaactgtagttcttattctaatgaactgctggtttctgatggcattttgttttcatgttacagTCTGATCCTCGTGTTAAAGAGAAGGTATTGGTGCTGATAGATACATGGCAAGACGTGTTTGGGGGATCACATGCAAGATATCCACAATACTATGCAGCAT
       ||| ||| | |        || |  ||||   ||   ||  ||||   | ||| ||   | || || |      || || | ||    | ||| ||||||||| |  |||| || || |||||||||||||| |  ||||| ||  |    ||||||||||||||||||||||||| ||
----gtaatggttcttccaaattggtctctctttctctctcccttgctctgcc--tctctaatcctaattggtctgatgcatatagCCGGACTTCCATGTCAAAGAGAAGATTCTGGTCCTTATCGATACATGGCAAGAGGCCTTTGGTGGCCCTAGGGCAAGATATCCACAATACTATGCAGGAT

upper sequence: GRMZM2G062953_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 3
-----------gttcaa-tat-gcttcatgcttgcaaaactgtagtt-cttattctaatgaactgctggtttctgatggcattttgttttcatg-ttacagTCTGATCCTCGTGTTAAAGAGAAGGTATTGGTGCTGATAGATACATGGCAAGACGTGTTTGGGGGATCACATGCAAGATATCCACAATACTATGCAGCAT
            ||||| ||    ||  |  || |  |  |  | ||  ||| |     ||    |  |||    || | ||||  | | ||   || ||| |||||   | ||| | ||||||| ||||| | ||||||||||| |||||||| |  ||||| ||| ||   ||||||||||||||||||||||| ||||
gtcagactgtcattcaagtaccatttttttgttccctagtttcatttatttacttatccgagaaacctgttc---atagtatttattctgcaaaattgcagCCTGATTTGCATGTCAGAGAGAAGATATTGATTCTGATAGATACTTGGCAAGAAGCTTTTGGAGGACCAAGGGCAAGATATCCACAATACTATGCTGCAT

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|211195280|gb|FK977671.1|FK977671
EST:     TTGCAGAGAGAGATATATTGCATGATATGGTGAAGATAGTGAAGAAAAAG                         TCTGATCCTCGTGTTAAAGAGAAGGTATTGGTGCTGATAGATACATGGCAA
genomic: TTGCAGAGAGAGATATATTGCATGATATGGTGAAGATAGTGAAGAAAAAGgttcaatatg ... catgttacagTCTGATCCTCGTGTTAAAGAGAAGGTATTGGTGCTGATAGATACATGGCAA
EST: gi|71759744|gb|DR957681.1|DR957681
EST:     TTGCAGAGAGAGATATATTGCATGATATGGTGAAGATAGTGAAGAAAAAG                         TCTGATCCTCGTGTTAAAGAGAAGGTATTGGTGCTGATAGATACATGGCAA
genomic: TTGCAGAGAGAGATATATTGCATGATATGGTGAAGATAGTGAAGAAAAAGgttcaatatg ... catgttacagTCTGATCCTCGTGTTAAAGAGAAGGTATTGGTGCTGATAGATACATGGCAA
EST: gi|149076223|gb|EE164821.2|EE164821
EST:     TTGCAGAGAGAGATATATTGCATGATATGGTGAAGATAGTGAAGAAAAAG                         TCTGATCCTCGTGTTAAAGAGAAGGTATTGGTGCTGATAGATACATGGCAA
genomic: TTGCAGAGAGAGATATATTGCATGATATGGTGAAGATAGTGAAGAAAAAGgttcaatatg ... catgttacagTCTGATCCTCGTGTTAAAGAGAAGGTATTGGTGCTGATAGATACATGGCAA
EST: gi|148952868|gb|EC898858.2|EC898858
EST:     TTGCAGAGAGAGATATATTGCATGATATGGTGAAGATAGTGAAGAAAAAG                         TCTGATCCTCGTGTTAAAGAGAAGGTATTGGTGCTGATAGATACATGGCAA
genomic: TTGCAGAGAGAGATATATTGCATGATATGGTGAAGATAGTGAAGAAAAAGgttcaatatg ... catgttacagTCTGATCCTCGTGTTAAAGAGAAGGTATTGGTGCTGATAGATACATGGCAA
EST: gi|211192891|gb|FK977670.1|FK977670
EST:     TTGCAGAGAGAGATATATTGCATGATATGGTGAAGATAGTGAAGAAAAAG                         TCTGATCCTCGTGTTAAAGAGAA
genomic: TTGCAGAGAGAGATATATTGCATGATATGGTGAAGATAGTGAAGAAAAAGgttcaatatg ... catgttacagTCTGATCCTCGTGTTAAAGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcttattctaatgaactgctggtttctgatggcattttgttttcatgttacagTCTGATCCTCGTGTTAAAGAGAAGGTATTGGTGCTGATAGATACATGGCAAGACGTGTTTGGGGGATCACATGCAAGATATCCACAATACTATGCAGCAT
                                    ttttgttttc  CT-rich tract
                                   attttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcaatatgcttcatgcttgcaaaactgtagttcttattctaatgaactgctggtttctgatggcattttgttttcatgttacagTCTGATCCTCGTGTTAAAGAGAAGGTATTGGTGCTGATAGATACATGGCAAGACGTGTTTGGGGGATCACATGCAAGATATCCACAATACTATGCAGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA