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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgtcattttcctccccgttctagtttatagatacacatattaagcatggcgagcaataatttgttgttttttgcattttagccaaaaaaaagagaagggtt...

Basic information

species Zea mays
transcript GRMZM2G135283_T04
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135283_T03 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 7
ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgt-cattttcctccccgttctagtttatagatacacatattaagcatggcgagcaataatttgttgttttttgcattttagccaaaaaaaagagaagggtt-
||||| ||||||||||| || |||  ||| ||||| |||||||||||||| ||||||||||||||||||||||| ||||||||||| |||||||| || | ||||||   | ||  ||| |    |  |  ||| | | |   ||    |   |  || |||| |   | | ||     |       ||  ||  
ACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAGgtgcaatgtcctccttat-ctgttttgttttaatgc-catttaacttattgaattctctatcattcttttataggtatgagttttcattggacaaaacgtgt

upper sequence: GRMZM2G135283_T03 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA18G27710.1 (Glycine max), 5'ss of exon 8
ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgt------------cattttcctccccgttctagt--ttatagatacacat-attaagcatggcgagcaataatttgttgtt-ttttgca-ttttagccaaaaaaaagagaagggtt----
||||| || || |||||||||||    ||||||||||||||||||||||| || |||||| | ||||| || ||||  ||||| || || |||||             |||||  ||   ||| |  |  || ||| ||||  | ||| |   |  |  |  |   |||  |||  | |||   |||| |  |    |||     |   |    
ACTGATACCAAAAAGATATCTGCTGTCTCAATATTTTTTGAGACAATGCCATATAGATTGAACGAAAGTACGGGATACATTGACTATGACCAGgtatcattgcaggatatttttatcatggttgtgatgcttttagctacatttcattgatattttcatgtcacccttttatgtcatcttgtggtttttgtgatgtgaaaatcttgaaatgcag

upper sequence: GRMZM2G135283_T03 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA14G36280.1 (Glycine max), 5'ss of exon 7
ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgtcatt---ttcctccccgttctagtttatagatacacatattaagcatggcgagcaat--aatttgttg--ttttttgcattttagccaaaaaaaagagaagggtt
|||||||| ||||||||||| ||    || ||||| ||||| |||||||| ||||||||| |||| |||||||| |  || ||||| || |||||   |   | ||      ||||   || | ||||  | |  | | ||  | ||    |  ||   || |   | |||  |||| ||         |  |       
ACTGACACCAAGAAGATATCGGCTGTATCTATATTCTTTGAAACAATGCCATACAGATTGAATGAGAGCACTGGTTATATCGATTATGACCAGgtaggtaggtaccattgtattctgtgttgtggatattctttcttatcaaagagaatcttttaagcagtcggactgtttctatttcagttgctgttcactg-------

upper sequence: GRMZM2G135283_T03 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA02G38160.2 (Glycine max), 5'ss of exon 7
ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgtcatt---ttcctccccgttctagtttatagatacacatattaagcatggcgagcaat--aatttgttg--ttttttgcattttagccaaaaaaaagagaagggtt
|||||||| ||||||||||| ||    || ||||||||||| |||||||| ||||||||| |||| |||||||| |  || ||||| || |||||   |   | ||      ||||   || | ||||    |  | | ||  |  |    |  ||   ||     | |||  |||| || ||  | | |          
ACTGACACCAAGAAGATATCAGCTGTATCTATATTTTTTGAAACAATGCCATACAGATTGAATGAGAGCACTGGTTATATCGATTATGACCAGgtaggtaggtaccattgtattctgtgttgtggatatttcttcttatcaaagaaaatcttttaagcagtcagactgtttctatttcagtcagtagagatta-------

upper sequence: GRMZM2G135283_T03 (Zea mays), 5'ss of exon 7
lower sequence: AT5G26780.3 (Arabidopsis thaliana), 5'ss of exon 7
ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgtcattt---tcctccccgttctagtttatagataca-catattaagcatggcgagcaataatttgttgttttttgcattttagccaaaaaaaa-----gagaagggtt------------------------------------------------------------------
|||||||| ||||| ||||| ||    || || ||||||||||||||||| |||||||||||||| | |||||| |  |||||||| || |||||   ||   || |  ||    ||| |||  | | || |||  ||    |  |   |||||     |||   | ||  ||| |  || | ||       |   | ||||                                                                  
ACTGACACGAAGAAAATATCGGCTGTATCCATCTTTTTTGAGACAATGCCATACAGATTGGATGAGAACACTGGTTACATTGATTATGACCAGgttggttagttcatagccagcttagcttaatgcttcaacattctatctttatc---caatataccattgagatatgggtttaatacatacaagcttttcgtttacggttcttatgttaagtaattgaacagtttttaaaccaaagtttatttatttgtgatacaataatttgcag

upper sequence: GRMZM2G135283_T03 (Zea mays), 5'ss of exon 7
lower sequence: Vv00s0211g00100.t01 (Vitis vinifera), 5'ss of exon 7
ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgtcattttcctccccgttctagtttatagatacacatattaagcatggcgagcaataatttgttgttttttgcattttagccaaaaaaaagagaagggtt--
|||||||| ||||| |||||||||   || |||||||||||||||||||| || |||||| |||| |||||||| |  ||||| || || ||||| | |||||     | | ||    |    | |   || |         ||||||   |||  | |  |||  | | ||        | | |    | ||  
ACTGACACCAAGAAAATATCTGCAGTGTCTATATTTTTTGAGACAATGCCATATAGATTGAATGAGAGCACTGGCTACATTGACTATGACCAGgtaactttccattttgct-tatagcaggagttcttttagttccatccctgagcaaatttttact-tagtttttactataatattttcacacaacttgtttaa

upper sequence: GRMZM2G135283_T03 (Zea mays), 5'ss of exon 7
lower sequence: Vv18s0001g07960.t01 (Vitis vinifera), 5'ss of exon 7
ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgt-cattttcctccccgttctagtttatagatacacatat-taagcatggcgagcaataatttgttgttttttgcattttagccaaaaaaaagagaagggtt
|| ||||| ||||||||||||||    || |||||||||||||||||||| ||||||||||||||||  |||||||  ||||| || || ||||| ||||| | || |  |     | | |   |     | | |     |  | |   |   | |     ||  ||||  |  |  |    |         |  
ACCGACACCAAGAAGATATCTGCTGTGTCTATATTTTTTGAGACAATGCCATACAGATTGGATGAAAAAACTGGATATATTGACTATGACCAGgtgcatttacatctctctctctctctctctctctctctctctctatctatctatggaagttcttccaattgatgcaaatatggtatgctaccatttttag--

upper sequence: GRMZM2G135283_T03 (Zea mays), 5'ss of exon 7
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 5'ss of exon 7
ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgtcattttcctccccgttctagtttatagatacacatattaagcatggcgagcaataatttgttgttttttgcattttagccaaaaaaaagagaagggtt--
|| ||||| ||||| |||||||||   || |||||||||||||||||||| || |||||| |||| |||||||| |  ||||| || || ||||| | |||||     | | ||    |    | |   || |         ||||||   |||  | |  |||  | | ||        | | |    | ||  
ACCGACACCAAGAAAATATCTGCAGTGTCTATATTTTTTGAGACAATGCCATATAGATTGAATGAGAGCACTGGCTACATTGACTATGACCAGgtaactttccattttgct-tatagcaggagttcttttagttccatccctgagcaaatttttact-tagtttttactataatattttcacacaacttgtttaa

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|67042253|gb|CO468508.1|CO468508
EST:     CTTACAGATTGCGATGAAAGCACTGGATTGATTGATTACGATCAG                         TTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
genomic: CTTACAGATTG-GATGAAAGCACTGGATTGATTGATTACGATCAGgtcattttcc ... ctatgtatagTTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
EST: gi|211349901|gb|FL349172.1|FL349172
EST:     CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG                         TTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
genomic: CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgtcattttcc ... ctatgtatagTTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
EST: gi|148973319|gb|EE024404.2|EE024404
EST:     CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG                         TTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
genomic: CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgtcattttcc ... ctatgtatagTTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
EST: gi|149012532|gb|EE042603.2|EE042603
EST:     CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG                         TTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
genomic: CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgtcattttcc ... ctatgtatagTTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
EST: gi|148946029|gb|EC891328.2|EC891328
EST:     CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG                         TTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
genomic: CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgtcattttcc ... ctatgtatagTTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
EST: gi|149048905|gb|EE048404.2|EE048404
EST:     CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG                         TTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
genomic: CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgtcattttcc ... ctatgtatagTTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
EST: gi|148958252|gb|EC904466.2|EC904466
EST:     CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG                         TTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
genomic: CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgtcattttcc ... ctatgtatagTTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
EST: gi|211286148|gb|FL173729.1|FL173729
EST:     A-TGCCTTACAGATTGGATGAAAGCACTGGGAT-GATTGATTACGATCAG                         TTGGAGAAAAGCGCTGTTCTTTTTAGGC-AAAGTTGAATCATGGCTGGTGC
genomic: AATGCCTTACAGATTGGATGAAAGCACTGG-ATTGATTGATTACGATCAGgtcattttcc ... ctatgtatagTTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGA-TCATTGCTGGTGC
EST: gi|60351519|gb|DN218492.1|DN218492
EST:     CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG                         TTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
genomic: CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgtcattttcc ... ctatgtatagTTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
EST: gi|71299012|gb|DR785498.1|DR785498
EST:     CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG                         TTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
genomic: CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgtcattttcc ... ctatgtatagTTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
EST: gi|148930308|gb|EE284699.2|EE284699
EST:     CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG                         TTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
genomic: CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgtcattttcc ... ctatgtatagTTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
EST: gi|60346600|gb|DN213573.1|DN213573
EST:     CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG                         TTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
genomic: CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgtcattttcc ... ctatgtatagTTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
EST: gi|67024112|gb|CO452861.1|CO452861
EST:     CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG                         TTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
genomic: CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgtcattttcc ... ctatgtatagTTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
EST: gi|148969981|gb|EE020895.2|EE020895
EST:     CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG                         TTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
genomic: CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgtcattttcc ... ctatgtatagTTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
EST: gi|149081312|gb|EE170425.2|EE170425
EST:     CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG                         TTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
genomic: CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgtcattttcc ... ctatgtatagTTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
EST: gi|148947246|gb|EC892606.2|EC892606
EST:     CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG                         TTGGAGAANAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
genomic: CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgtcattttcc ... ctatgtatagTTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
EST: gi|149089957|gb|EE179246.2|EE179246
EST:     CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG                         TTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
genomic: CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgtcattttcc ... ctatgtatagTTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
EST: gi|148945831|gb|EC891120.2|EC891120
EST:     CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG                         TTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA
genomic: CAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgtcattttcc ... ctatgtatagTTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCA

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: 45 (upstream exon), 49 (downstream exon)
Score: 456

ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgtcattttcc ... ctatgtatagTTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCAAGTGCATATGCTCGGCTATATGATTATGACCGTATGCGGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 572

ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgtcattttcc ... ctatgtatagTTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCAAGTGCATATGCTCGGCTATATGATTATGACCGTATGCGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 487

ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgtcattttcc ... ctatgtatagTTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCAAGTGCATATGCTCGGCTATATGATTATGACCGTATGCGGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 731

ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgtcattttcc ... ctatgtatagTTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCAAGTGCATATGCTCGGCTATATGATTATGACCGTATGCGGAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGgtcattttcctccccgttctagtttatagatacacatattaagcatggcgagcaataatttgttgttttttgcattttagccaaaaaaaagagaagggtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaaa