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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacagcactgctgctgcacagcggagtgttgtgaagttccattcctatcggaaacaatctgtgcgcgttgattgctaaaagtgatctgtgttcctaacagGCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCGACGCACAACATCAACGTGAACAAGATCTTCAAGTTCATCACGGCCAAGC

Basic information

species Zea mays
transcript GRMZM2G027344_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027344_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g33850.2 (Oryza sativa), 3'ss of exon 5
tacagcactgctgctgcacagcggagtgttgtgaagttccattcctatcggaaacaatctgtgcgcgttgattgctaaaagtgatctgtgttcctaa----cagGCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCGACGCACAACATCAACGTGAACAAGATCTTCAAGTTCATCACGGCCAAGC
 | |   | |   ||  |   |||||    || |  |   |    | |      |  | | | |  |||   || |  | |   | | | |||  ||    |||||||| |||||||| ||||||||||||||||||||||||||||| ||| |||||||||||||||||||||||||||||||||||||||||||||||||||
catatgtcagtcccttaaagtcggaggacagtaagttagaaggtttttttc---cgttgtattcttgttt-ctgatggaggattttttttttctgaaatttcagGCCAGGGCATACGCGAGAGCGATGAAGGCGACCCTCTTCTTCTCCAGCTCGACGCACAACATCAACGTGAACAAGATCTTCAAGTTCATCACGGCCAAGC

upper sequence: GRMZM2G027344_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA06G46250.1 (Glycine max), 3'ss of exon 3
tacagcactgctgctgcacag-cggagtgttgtgaagttccattcctatcggaaacaatctgtgcg-cgttgattgctaaaagtgatctgtgttcct-aacagGCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCGACGCACAACATCAACGTGAACAAGATCTTCAAGTTCATCACGGCCAAGC
||   ||  | |  |||| || |      || | | |||   |    ||  ||    || |    |  | |||| |      | ||| ||||    | ||||||| |||   || ||||  ||  | || || ||| | ||||| || || || ||  |||||||||| |||||||||||||||||||||||||| || || |
taatacatcgattatgcaaagGCAAGAAATTCTCAGGTTT--TCAAGATAAGATTTGATGTTGATGATGATGAT-GTGTGTTGCGATGTGTGACATTGAACAGGCAAGAAATTATGCAAAGGCCCTCAATGCCACCTTGTTCTTTTCAAGTGCAACCTACAACATCAATGTGAACAAGATCTTCAAGTTCATCACTGCTAAAC

upper sequence: GRMZM2G027344_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA06G46120.1 (Glycine max), 3'ss of exon 5
------tacagcactgctgctgcacagcggagtgttgtgaagttccattcctatcggaaacaatctgtgcgcgttgattgctaaaagtgatctgtgttcctaacagGCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCGACGCACAACATCAACGTGAACAAGATCTTCAAGTTCATCACGGCCAAGC
      | |      |    | || |   |         || |  ||    |    || |  || ||     ||   || | |   ||||  |        ||||||| |||  ||| ||||  ||  | || || ||| | ||||| || || || ||  |||||||||| ||||||||||||||||||||| |||| || || |
ttggaatgctatgtaggctttccaaaatagctaaagaaaaattctcaggttttcaagataagatttgatgatgtgtgttacgatgtgtgacat------tgaacagGCAAGAAAATATGCAAAGGCCCTCAATGCCACCTTGTTCTTTTCAAGTGCAACCTACAACATCAATGTGAACAAGATCTTCAAGTTCGTCACTGCTAAAC

upper sequence: GRMZM2G027344_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA12G10670.1 (Glycine max), 3'ss of exon 5
-tacagcactgctgctgcacagcggagtgttgtgaagttccattcctatcggaaacaatctgtgcgcgttgattgctaaaagtgatctgtgttcct-aacagGCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCGACGCACAACATCAACGTGAACAAGATCTTCAAGTTCATCACGGCCAAGC
 |  |   ||      ||    |    |      ||  | | |   | |   | | ||  | ||   | |||||  |    ||| | ||||    | ||||||| |||  ||| ||||  ||  | || || ||| | ||||| || || || ||  |||||||||| ||||| |||||||||||||||||||| || || |
ttggaatgctatgcaggctttccaagatagcaaaaaaattcttatgttttcaagataagatttg-atgatgatttgtgtt-gtgttttgtgacattgaacagGCAAGAAAATATGCAAAGGCCCTCAATGCCACCTTGTTCTTTTCAAGTGCAACCTACAACATCAATGTGAATAAGATCTTCAAGTTCATCACTGCTAAAC

upper sequence: GRMZM2G027344_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA14G02890.1 (Glycine max), 3'ss of exon 5
tacag--cactgctgctgcacagcggagtgttgtgaagttccattcctatcggaaacaatctgtgcgcgttgattgctaaaagtgatctgtgttcctaa--cagGCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCGACGCACAACATCAACGTGAACAAGATCTTCAAGTTCATCACGGCCAAGC
 ||||  |||  ||    |       |  ||    |       ||  ||||    ||| ||  ||    || |  | | ||  ||    |       ||  ||||| || ||||| ||||| ||||||||||| ||||| ||||| || || || || |||||||| || || ||||| || |||||||| |||| ||||||||
cacagttcacgactttcactttaaataaagtcaatagtacaactttttatc----acattccttggcttttcaaagtttaacttggaacgacacataaatacagGCAAGGGCATATGCAAGGGCGATGAAGGCAACCCTTTTCTTTTCAAGTGCAACCCACAACATAAATGTCAACAAAATTTTCAAGTTTATCATGGCCAAGC

upper sequence: GRMZM2G027344_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA02G45870.1 (Glycine max), 3'ss of exon 5
tacagcactgctgctgcacagcggagtgttgtgaagttccattcctatcggaaacaatctgtgcgcgttga----ttgctaaaagtgat-ctgtgttccta-acagGCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCGACGCACAACATCAACGTGAACAAGATCTTCAAGTTCATCACGGCCAAGC
      |   ||       |    | |  |   |  ||   ||  ||      ||| |   ||    || |    ||  | ||  || | | | |     | |||||| || ||||| ||||| ||||||||||| ||||| ||||| || || || || |||||||| || || ||||| || |||||||| |||| ||||||||
------ataactttaaataaagttaatagtactactttttttttttaattatcacattacttggcttttcaaaatttaattaacttggtacggcgcataaatacagGCAAGGGCATATGCAAGGGCGATGAAGGCAACCCTTTTCTTTTCAAGTGCAACCCACAACATAAATGTCAACAAAATTTTCAAGTTTATCATGGCCAAGC

upper sequence: GRMZM2G027344_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA02G45870.3 (Glycine max), 3'ss of exon 5
-------------------------------tacagcactgctgctgcacagcgg-agtgttgtgaagttccattcctatcggaaacaatctgtgcgcgttga----ttgctaaaagtgat-ctgtgttccta-acagGCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCGACGCACAACATCAACGTGAACAAGATCTTCAAGTTCATCACGGCCAAGC
                                || |   |     |  | |  |  | |  |   |  ||   ||  ||      ||| |   ||    || |    ||  | ||  || | | | |     | |||||| || ||||| ||||| ||||||||||| ||||| ||||| || || || || |||||||| || || ||||| || |||||||| |||| ||||||||
gtctcactactttctttttttggcagaaattcacggttataactttaaataaagttaatagtactactttttttttttaattatcacattacttggcttttcaaaatttaattaacttggtacggcgcataaatacagGCAAGGGCATATGCAAGGGCGATGAAGGCAACCCTTTTCTTTTCAAGTGCAACCCACAACATAAATGTCAACAAAATTTTCAAGTTTATCATGGCCAAGC

upper sequence: GRMZM2G027344_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT5G54840.1 (Arabidopsis thaliana), 3'ss of exon 5
-----------------------------------------tacagcactgctgctgcacagcg-------gagtgttgtgaagttcca--ttcctatcggaaacaatctgtgcgcgttgattgctaaaagtgatctgtgtt-cctaacagGCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCGACGCACAACATCAACGTGAACAAGATCTTCAAGTTCATCACGGCCAAGC
                                         ||   | ||  |  |      ||       ||   ||  ||  || |   ||  | |   ||   || | |        || | |||    | ||| | |    ||  |||| |||||||| || |  | |||||| ||| |  | |||||||| || ||||| |||||||| || ||||||||||||||||| |||||   ||| |  |
gtaataccaatcatacaacttaatcataccacgttaccaattaagacccttttcatattttacgttttcatgatgatttagacatttcgatttattgtgataattcatttctataaaaaaatagttaatttggttctatatgatttattagGCAAGAGCATATGCGAAGGTGATGAATGCGTCATTGTTCTTCTCAAGTGCGACACACAACATAAATGTGAACAAGATCTTCAAATTCATTTTGGCTAGAC

upper sequence: GRMZM2G027344_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv19s0014g00960.t01 (Vitis vinifera), 3'ss of exon 5
tacagcactgctgctgcacagcggagtgttgtgaagttccattcctatcggaaacaatctg---tgcgcgttg-attgctaaaagtgatctgtgttcctaa--cagGCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCGACGCACAACATCAACGTGAACAAGATCTTCAAGTTCATCACGGCCAAGC
      |  |    |  | || | |   |    |      |          |||||   ||     | | ||| | | |||   |  | |  | ||  |||  ||||| |||| ||| || || || |||||||| || ||||||||||| || || || |||||||| || |||||||| |||||||| ||||||| ||||||||
----tgaaagaaaataaa-agagaaaaatcagaagaaaagaaaaaggcaaaaaacagattgattctcacattgtaatcctactcgc-acccattttgttaatgcagGCAAGAGGATATGCCAGGGCTATGAAGGCAACACTCTTCTTCTCAAGTGCCACACACAACATAAATGTGAACAAAATCTTCAAATTCATCATGGCCAAGC

upper sequence: GRMZM2G027344_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv12s0059g02280.t01 (Vitis vinifera), 3'ss of exon 5
---tacagcactgctgctgcacagcggagtgttgtgaagttccattcctatcggaaacaatctgtgcgcgttgattgctaaaagtgatctgtgttcctaacagGCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCGACGCACAACATCAACGTGAACAAGATCTTCAAGTTCATCACGGCCAAGC
   | |   |||   | ||  |  |    | || | ||  |  |  |  ||   |||        | |      ||  || | ||   |  ||||  |  ||||| ||||| ||||| |  ||  | || || || ||||||||||||||||| ||  ||||||| |||||||||||||||||||| |||||||| || || |
atttgcttgact-taggtgggccccttgctcttctaaacatatagacgcattttaaagtcataaggagaaagagttattacatgta--ccttgtttttggcagGCAAGAGCGTACGCTAAGGCCCTAAATGCAACGCTCTTCTTCTCGAGCGCAACCTACAACATAAACGTGAACAAGATCTTCAAATTCATCACAGCAAAAC

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|26455329|gb|CA826912.1|CA826912
EST:     ATGACTTTGCCCAGCTTCCTCTTGAAATGCAATGGACCATTGTTAACCAG                         GCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCG
genomic: ATGACTTTGCCCAGCTTCCTCTTGAAATGCAATGGACCATTGTTAACCAGgtgagcagtg ... ttcctaacagGCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCG
EST: gi|89106664|gb|DY576881.1|DY576881
EST:     ATGACTTTGCCCAGCTTCCTCTTGAAATGCAATGGACCATTGTTAACCAG                         GCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCG
genomic: ATGACTTTGCCCAGCTTCCTCTTGAAATGCAATGGACCATTGTTAACCAGgtgagcagtg ... ttcctaacagGCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCG
EST: gi|21330939|gb|BQ486320.1|BQ486320
EST:     ATGACTTTGCCCAGCTTCCTCTTGAAATGCAATGGACCATTGTTAACCAG                         GCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCG
genomic: ATGACTTTGCCCAGCTTCCTCTTGAAATGCAATGGACCATTGTTAACCAGgtgagcagtg ... ttcctaacagGCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCG
EST: gi|7145324|gb|AW506805.1|AW506805
EST:     AATGGACCATTGTTAACCAG                         GCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCG
genomic: AATGGACCATTGTTAACCAGgtgagcagtg ... ttcctaacagGCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCG
EST: gi|7145325|gb|AW506806.1|AW506806
EST:     ATGACTTTGCCCAGCTTCCTCTTGAAATGCAATGGACCATTGTTAACCAG                         GCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCG
genomic: ATGACTTTGCCCAGCTTCCTCTTGAAATGCAATGGACCATTGTTAACCAGgtgagcagtg ... ttcctaacagGCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCG
EST: gi|5928684|gb|AW055901.1|AW055901
EST:     ATGACTTTGCCCAGCTTCCTCTTGAAATGCAATGGACCATTGTTAACCAG                         GCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCG
genomic: ATGACTTTGCCCAGCTTCCTCTTGAAATGCAATGGACCATTGTTAACCAGgtgagcagtg ... ttcctaacagGCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCG

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: 46 (upstream exon), 40 (downstream exon)
Score: 9

ACGGCTATTCCAATCCTAATCGGGACAAAGTTCGATGACTTTGCCCAGCTTCCTCTTGAAATGCAATGGACCATTGTTAACCAGgtgagcagtg ... ttcctaacagGCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCGACGCACAACATCAACGTGAACAAGATCTTCAAGTTCATCACGGCCAAGC


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 35

ACGGCTATTCCAATCCTAATCGGGACAAAGTTCGATGACTTTGCCCAGCTTCCTCTTGAAATGCAATGGACCATTGTTAACCAGgtgagcagtg ... ttcctaacagGCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCGACGCACAACATCAACGTGAACAAGATCTTCAAGTTCATCACGGCCAAGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 42

ACGGCTATTCCAATCCTAATCGGGACAAAGTTCGATGACTTTGCCCAGCTTCCTCTTGAAATGCAATGGACCATTGTTAACCAGgtgagcagtg ... ttcctaacagGCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCGACGCACAACATCAACGTGAACAAGATCTTCAAGTTCATCACGGCCAAGC


Block sizes: 25 (upstream exon), 47 (downstream exon)
Score: 35

ACGGCTATTCCAATCCTAATCGGGACAAAGTTCGATGACTTTGCCCAGCTTCCTCTTGAAATGCAATGGACCATTGTTAACCAGgtgagcagtg ... ttcctaacagGCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCGACGCACAACATCAACGTGAACAAGATCTTCAAGTTCATCACGGCCAAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcggaaacaatctgtgcgcgttgattgctaaaagtgatctgtgttcctaacagGCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCGACGCACAACATCAACGTGAACAAGATCTTCAAGTTCATCACGGCCAAGC
                           tgctaaa  putative branch site (score: 35)
                                           tgttcct  putative PPT
      aaacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacagcactgctgctgcacagcggagtgttgtgaagttccattcctatcggaaacaatctgtgcgcgttgattgctaaaagtgatctgtgttcctaacagGCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCGACGCACAACATCAACGTGAACAAGATCTTCAAGTTCATCACGGCCAAGC

tacagca
- - - - -gctgctg
- - - - - - - - - - - - - tgttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - -aaacaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgattgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatctg