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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactttgaggtgctgggtcatgtagagatataatctgcacagaagccttatgttaacctgtgcacccaagtccctaattactttctgtgttatcctacagACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACAAGCATGCTGTTCCGAAACCGAAAGACCAATGCAGTAAGCCACTACAACT

Basic information

species Zea mays
transcript GRMZM2G118208_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118208_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g15690.2 (Oryza sativa), 3'ss of exon 2
aactttgaggtgctgggtcatgtagagatataatctgcacagaagccttatgttaacctgtgcacccaagtccctaattactttctgtgttatcctacagACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACAAGCATGCTGTTCCGAAACCGAAAGACCAATGCAGTAAGCCACTACAACT---------------------------------------------
                                            |  |  | |||   |||  |  |       |   ||   |   | | |   | |||| |||||| ||||||||||||||||||| || ||||||||  | || || |||||||| ||||| || || |||||  |||||||||||||||| || ||                                             
-------------------------------------------cgtttccttttaggttgt-tattctcacttgtgtctaaactactt-tcaatttccagatactatggtgaaatttgcttgctttgagacaattgttgaattagTATATAAGCATGCAGTTCCAAAGCCAAAAGATGAATGCAGTAAGCCACTCCAGCTAGCAGTGAGCTTTGCAGGGGGATATATTGCAGGAGTCTTCTGTGC

upper sequence: GRMZM2G118208_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g15690.1 (Oryza sativa), 3'ss of exon 3
aactttgaggtgctgggtcatgtagagatataatctgcacagaagcc---ttatgttaacctgtgcacccaagtccctaattactttctgtgttatcctacagACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACAAGCATGCTGTTCCGAAACCGAAAGACCAATGCAGTAAGCCACTACAACT
        | | ||  |||  ||| ||||   | |    |  | |||   |  | |||   |||  |  |       |   ||   |   | | |   | |||| |||||| ||||||||||||||||||| || ||||||||  | || || |||||||| ||||| || || |||||  |||||||||||||||| || ||
-gtaagatgctactaagtcccgtacagatgccagcaattcttatgccgtttccttttaggttgt-tattctcacttgtgtctaaactactt-tcaatttccagATACTATGGTGAAATTTGCTTGCTTTGAGACAATTGTTGAATTAGTATATAAGCATGCAGTTCCAAAGCCAAAAGATGAATGCAGTAAGCCACTCCAGCT

upper sequence: GRMZM2G118208_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT5G14040.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------aac---tttgaggtgctgggtcatgtagagatataatctgcacagaagccttatgttaacctgtgcacccaa--gtccctaattactttctgtgttatcctacagACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACAAGCATGCTGTTCCGAAACCGAAAGACCAATGCAGTAAGCCACTACAACT
                       |||   ||  |    ||   |  | |     | |  | |    |  |  | |||||    || |  |  |||  |    | || | | ||| ||  ||  |||||||||||||||||| ||||||| |||||| || |||||||||||| | |||||| | ||  | || || || ||     | ||||| ||    || |||||
gtaagttctggcctctattttgcaacctgttgcacaatctttttttttttttttttttgtttattgatgaaacatatgtagttctttaaaagcaaaaggtggtgatga-tatctatga-attttacagACACTATGATGAAGTTTGCTTCCTTTGAGACCATTGTTGAGATGATTTACAAGTACGCAATCCCCAACCCAAAGAGTGAGTGCAGCAAAGGTCTGCAACT

upper sequence: GRMZM2G118208_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv14s0068g01260.t01 (Vitis vinifera), 3'ss of exon 3
aactttgaggtgctgggtc-atgtagagatataatctgcacagaagccttatgttaacctgtgcacccaagtccctaattactttctgtgttatcctacagACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACAAGCATGCTGTTCCGAAACCGAAAGACCAATGCAGTAAGCCACTACAACT
   ||     ||    |   || ||      |  | ||  |         |||||||  |        ||     |||   | |  ||  || |  | |||| || ||||||||||||||||  ||||| ||||||||||||||| | |||||| ||||  |||| |  ||||| ||||| ||||||||  | || || ||
-gtttctccttgtcatgctgatataattggcttttttgggctttgcgtaaatgttaatgttcattagaaatcttataaaatcataatggttttttgtgcagATACAATGATGAAATTTGCTTCTTTTGAGACTATTGTTGAGATGCTTTACAAGTATGCCATTCCTACTCCGAAGGACCAGTGCAGTAAAACTCTGCAGCT

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|60347958|gb|DN214931.1|DN214931
EST:     GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT                         ACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACA
genomic: GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCTgtaagtcaaa ... tatcctacagACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACA
EST: gi|71759052|gb|DR956989.1|DR956989
EST:     CTTTGGGCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT                         ACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACA
genomic: CTTTGGGCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCTgtaagtcaaa ... tatcctacagACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACA
EST: gi|76281616|gb|DV021184.1|DV021184
EST:     GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT                         ACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACA
genomic: GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCTgtaagtcaaa ... tatcctacagACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACA
EST: gi|101382650|gb|EB813379.1|EB813379
EST:     GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT                         ACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACA
genomic: GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCTgtaagtcaaa ... tatcctacagACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACA
EST: gi|74245908|gb|DT653822.1|DT653822
EST:     GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT                         ACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACA
genomic: GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCTgtaagtcaaa ... tatcctacagACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACA
EST: gi|71417465|gb|DR804063.1|DR804063
EST:     GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT                         ACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACA
genomic: GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCTgtaagtcaaa ... tatcctacagACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACA
EST: gi|60354997|gb|DN221970.1|DN221970
EST:     GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT                         ACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACA
genomic: GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCTgtaagtcaaa ... tatcctacagACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACA
EST: gi|71767406|gb|DR965343.1|DR965343
EST:     GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT                         ACACTATGATGAAATTTGCTTGCTTT
genomic: GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCTgtaagtcaaa ... tatcctacagACACTATGATGAAATTTGCTTGCTTT
EST: gi|91874483|gb|EB404440.1|EB404440
EST:     GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT                         ACACTATGATGAAATTTGCTTGCTTTG
genomic: GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCTgtaagtcaaa ... tatcctacagACACTATGATGAAATTTGCTTGCTTTG
EST: gi|37398965|gb|CF636804.1|CF636804
EST:     GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT                         ACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACA
genomic: GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCTgtaagtcaaa ... tatcctacagACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACA
EST: gi|78544938|gb|DV622436.1|DV622436
EST:     GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT                         ACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACA
genomic: GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCTgtaagtcaaa ... tatcctacagACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACA
EST: gi|67010579|gb|CO439328.1|CO439328
EST:     GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCT                         ACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACA
genomic: GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCTgtaagtcaaa ... tatcctacagACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 45

GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCTgtaagtcaaa ... tatcctacagACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACAAGCATGCTGTTCCGAAACCGAAAGACCAATGCAGTAAGCCACTACAACT


Block sizes: 33 (upstream exon), 48 (downstream exon)
Score: 64

GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCTgtaagtcaaa ... tatcctacagACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACAAGCATGCTGTTCCGAAACCGAAAGACCAATGCAGTAAGCCACTACAACT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 67

GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCTgtaagtcaaa ... tatcctacagACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACAAGCATGCTGTTCCGAAACCGAAAGACCAATGCAGTAAGCCACTACAACT


Block sizes: 14 (upstream exon), 46 (downstream exon)
Score: 19

GCTTTACAAAGGTCTACTTCCTCTTTGGGGCCGCCAAGTTCCCTgtaagtcaaa ... tatcctacagACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACAAGCATGCTGTTCCGAAACCGAAAGACCAATGCAGTAAGCCACTACAACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttatgttaacctgtgcacccaagtccctaattactttctgtgttatcctacagACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACAAGCATGCTGTTCCGAAACCGAAAGACCAATGCAGTAAGCCACTACAACT
                                            ttatcct  CT-rich tract
                             taattacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactttgaggtgctgggtcatgtagagatataatctgcacagaagccttatgttaacctgtgcacccaagtccctaattactttctgtgttatcctacagACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACAAGCATGCTGTTCCGAAACCGAAAGACCAATGCAGTAAGCCACTACAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - ggtgctg
- - - - - - - - - catgtag
- - - - - - - - - - - - - - - - atctgca
- - - - - - - - - - - - - - - - - - - -cagaagc
- - - - - - - - - - - - - - - - - - - - - - - -ttatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgcacc