Skip to another splice site:
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttatagttcaaactaccctttaggaatatgaatctcaagtattggcaattttaaacgaacacttcaggcacggtatctgacgggtattgtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACATTACACCAACAGCTTTGGACCGGTGGGAGAAGAGACTTGAGGATCTGTT

Basic information

species Zea mays
transcript GRMZM2G300348_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G300348_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g51290.3 (Oryza sativa), 3'ss of exon 2
ctttatagttcaaactaccct-ttaggaatatgaatctcaagtattggcaattttaaacgaacacttc-aggcacggtatctgacgggtattgtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACATTACACCAACAGCTTTGGACCGGTGGGAGAAGAGACTTGAGGATCTGTT
   |  |  | || |    ||  ||  ||| | || ||     ||  || | || |  |    | ||  |     | | | |  |   | || ||| ||||||||||||||||||||||||||||||||||||||| ||||| |||    |||| |||||  ||||  ||||||||||||||||||| ||||| ||||| ||
aaatgaatatgaatccgtactactaacaatttcaaacttttaaatgagctagttcaggcatgaattttgaaatctgatgtatacct--ttttttttttgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGACCAAATGCCTCGCACATCACACCGTCAGCCCTGGACCGGTGGGAGAAGAGGCTTGATGATCTCTT

upper sequence: GRMZM2G300348_T04 (Zea mays), 3'ss of exon 2
lower sequence: Vv04s0079g00680.t01 (Vitis vinifera), 3'ss of exon 3
---ctttatagttcaaactaccctttaggaatatgaatctcaagtattggcaattttaaacgaacacttcaggcacggtatctgacgggtattgtttct---gcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACATTACACCAACAGCTTTGGACCGGTGGGAGAAGAGACTTGAGGATCTGTT
    ||| ||  |  |   ||  |  |  | |   |  || ||  |  | | |     |      |  |        || ||| | |  | |   | |     ||||||||||| |||| |||||||||||||| |||||||| || ||     |||| || |||||||| |||||  ||||||||   ||  | || ||||| ||
gaattttgtaaat--atgcacaatacacaagttcaatactgaaacaaagacga----gaggatttatattctcttttgtttcttatgattctctctccatgaacagTGTGGTGTCGGAGAACAGATGAGCTTGTTGATGGGCCTAATGCATCACACATAACCCCAACAGCCTTGGATAGGTGGGAGTCAAGGTTGGAAGATCTTTT
















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|148973689|gb|EE024811.2|EE024811
EST:     AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG                         TGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCCAAACGCCA-CTAC
genomic: AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATGgtatctgtct ... gtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCC-AAACGCCAACTAC
EST: gi|91054433|gb|EB164851.1|EB164851
EST:     AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG                         TGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
genomic: AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATGgtatctgtct ... gtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
EST: gi|211364023|gb|FK959512.1|FK959512
EST:     AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGC-ATCTATG                         TGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCC
genomic: AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATGgtatctgtct ... gtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCC
EST: gi|74241172|gb|DT649086.1|DT649086
EST:     AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG                         TGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
genomic: AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATGgtatctgtct ... gtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
EST: gi|148946928|gb|EC892212.2|EC892212
EST:     AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG                         TGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
genomic: AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATGgtatctgtct ... gtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
EST: gi|93281436|gb|EB673700.1|EB673700
EST:     AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG                         TGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
genomic: AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATGgtatctgtct ... gtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
EST: gi|149008706|gb|EE040900.2|EE040900
EST:     AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG                         TGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
genomic: AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATGgtatctgtct ... gtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
EST: gi|94472244|gb|EB701202.1|EB701202
EST:     AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG                         TGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
genomic: AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATGgtatctgtct ... gtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
EST: gi|101401215|gb|EB822286.1|EB822286
EST:     AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG                         TGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
genomic: AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATGgtatctgtct ... gtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
EST: gi|91877248|gb|EB407205.1|EB407205
EST:     AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG                         TGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
genomic: AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATGgtatctgtct ... gtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
EST: gi|148995759|gb|EE034988.2|EE034988
EST:     AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG                         TGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
genomic: AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATGgtatctgtct ... gtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
EST: gi|78104640|gb|DV523058.1|DV523058
EST:     AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG                         TGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
genomic: AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATGgtatctgtct ... gtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
EST: gi|76911964|gb|DV164511.1|DV164511
EST:     AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG                         TGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
genomic: AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATGgtatctgtct ... gtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
EST: gi|76916879|gb|DV166586.1|DV166586
EST:     AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG                         TGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
genomic: AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATGgtatctgtct ... gtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
EST: gi|71447701|gb|DR828751.1|DR828751
EST:     AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG                         TGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
genomic: AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATGgtatctgtct ... gtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
EST: gi|71775307|gb|DR973185.1|DR973185
EST:     AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG                         TGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
genomic: AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATGgtatctgtct ... gtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
EST: gi|211364025|gb|FK959514.1|FK959514
EST:     AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG                         TGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAA
genomic: AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATGgtatctgtct ... gtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAA
EST: gi|50325756|gb|CO520882.1|CO520882
EST:     AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG                         TGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
genomic: AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATGgtatctgtct ... gtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
EST: gi|93016198|gb|EB641718.1|EB641718
EST:     AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG                         TGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
genomic: AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATGgtatctgtct ... gtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
EST: gi|67028270|gb|CO457019.1|CO457019
EST:     AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG                         TGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
genomic: AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATGgtatctgtct ... gtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
EST: gi|71444100|gb|DR825150.1|DR825150
EST:     AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG                         TGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
genomic: AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATGgtatctgtct ... gtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
EST: gi|149073532|gb|EE161835.2|EE161835
EST:     AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG                         TGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
genomic: AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATGgtatctgtct ... gtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
EST: gi|149075800|gb|EE164333.2|EE164333
EST:     AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG                         TGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA
genomic: AACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATGgtatctgtct ... gtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACA

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: 25

GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATGgtatctgtct ... gtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACATTACACCAACAGCTTTGGACCGGTGGGAGAAGAGACTTGAGGATCTGTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 164

GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATGgtatctgtct ... gtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACATTACACCAACAGCTTTGGACCGGTGGGAGAAGAGACTTGAGGATCTGTT


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

GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATGgtatctgtct ... gtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACATTACACCAACAGCTTTGGACCGGTGGGAGAAGAGACTTGAGGATCTGTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 241

GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATGgtatctgtct ... gtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACATTACACCAACAGCTTTGGACCGGTGGGAGAAGAGACTTGAGGATCTGTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcaattttaaacgaacacttcaggcacggtatctgacgggtattgtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACATTACACCAACAGCTTTGGACCGGTGGGAGAAGAGACTTGAGGATCTGTT
                               atctgac  putative branch site (score: 241)
                                           ttgtttct  putative PPT
     ttttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttatagttcaaactaccctttaggaatatgaatctcaagtattggcaattttaaacgaacacttcaggcacggtatctgacgggtattgtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACATTACACCAACAGCTTTGGACCGGTGGGAGAAGAGACTTGAGGATCTGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT