Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgcatccttttcttaacagagttattaaatcaaacatatgcttttttcttcatgctctacttgctttgatttctgataaacctttctatcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCTGGGTGAG

Basic information

species Zea mays
transcript GRMZM5G851698_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G851698_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 3'ss of exon 2
attgcatccttttcttaacagagttattaaatca--aacatatgcttttttcttcatgctctacttgctttgatttctgataaacctttctatcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCTGGGTGAG
 | |   |||||   |  |    || |||  | |  |    |   |  |||     || |||      || ||| ||||||   ||||| |||  |||  || ||||| |||| ||||   |||||||| |||||||||||||| ||||||||||| |||
gtgggtgcctttcaatgtctaccttgttagctgatgactgaacattagtttgagtttgttctgtaaaattggatatctgatg--cctttgtatgtactgcagGCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAG

upper sequence: GRMZM5G851698_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA07G31840.2 (Glycine max), 3'ss of exon 2
-attgcatccttttcttaacagagttattaaatcaaacatatgcttttttcttcat-gctctacttgctttgatttctgataaacctttctatcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCTGGGTGAG
  | ||       | | |||        |   ||   | |   ||| |  |||||   ||  ||   | |   ||  ||        | ||||  | |  || || || ||||  |||   |||||||||||||||||   |||||||||||||||||||
tttagcggggaaatttgaacccg--cgatctctccccccttcccttctcccttcaccactggaccaacctctgttattgtattcttatgctatatattgcagTCGAGCATTTTGGGACAAGAGGATCTCCCAGGAGGTTCTTGGTGATGCTCTGGGTGAG

upper sequence: GRMZM5G851698_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 2
attgcatccttttcttaacagagttattaaatcaaac-atatgcttttttcttcatgctctactt-gctttgatttctgataaacctttctatcaac-tatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCTGGGTGAG
    ||   |  ||  || |   || |||  |  | | |||   | |  ||||  | || |||   |  |    || |  ||    |   | |   | |  || || || |||| ||||   |||||||| |||||||||||||| ||||| |||||||||
--ctcaaagtcctcccaaaatttttcttatttttacccataaagtatcatctt-gtactttacagaggatcagcttttcttatttttgagtgttgtcatgcagGCGAGCATTTTTTGACAAGAGGATCTCACAGGAGGTCAGTGGAGATGCACTGGGTGAG

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|149077949|gb|EE166681.2|EE166681
EST:     CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT                         ACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
EST: gi|76923081|gb|DV169325.1|DV169325
EST:     CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT                         ACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
EST: gi|211068384|gb|FL392622.1|FL392622
EST:     CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT                         ACGTGCCTTTTATGACCGAA-GATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
EST: gi|211542573|gb|FL410011.1|FL410011
EST:     CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT                         ACGTGCCTTTTATAGACCGAA-GATCTCCCAGGAGGTCAGTGGTGATGCTC
genomic: CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTAT-GACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTC
EST: gi|15312778|gb|BI478369.1|BI478369
EST:     CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT                         ACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
EST: gi|211431422|gb|FL393492.1|FL393492
EST:     CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT                         ACGTGCCTTTTATGACCGAAG-ATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
EST: gi|20300566|gb|BQ163509.1|BQ163509
EST:     CCGTCTACCGGGTGCCAGAAGATGCTGGAAATCGATGACGACCAGAAACT                         ACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
EST: gi|78079211|gb|DV507623.1|DV507623
EST:     CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT                         ACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
EST: gi|5081006|gb|AI738268.1|AI738268
EST:     CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT                         GCGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
EST: gi|148969224|gb|EE019976.2|EE019976
EST:     CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT                         ACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
EST: gi|67016348|gb|CO445097.1|CO445097
EST:     CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT                         GCGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
EST: gi|78024666|gb|DV493053.1|DV493053
EST:     CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT                         GCGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
EST: gi|29946749|gb|CB816306.1|CB816306
EST:     CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT                         ACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
EST: gi|19058404|gb|BM737071.1|BM737071
EST:     CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT                         ACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
EST: gi|21987949|gb|BQ779477.1|BQ779477
EST:     CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT                         GCGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
EST: gi|22819122|gb|BU499212.1|BU499212
EST:     CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT                         GCGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
EST: gi|15632345|gb|BI679438.1|BI679438
EST:     CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT                         ACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
EST: gi|148966135|gb|EE017078.2|EE017078
EST:     CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT                         ACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
EST: gi|71428551|gb|DR809601.1|DR809601
EST:     CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT                         ACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
EST: gi|19057795|gb|BM736462.1|BM736462
EST:     CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT                         ACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
EST: gi|148955068|gb|EC900579.2|EC900579
EST:     CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT                         ACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
EST: gi|78075296|gb|DV503730.1|DV503730
EST:     GAAGCTGGAAATCGATGACGACCAGAAACT                         ACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: GAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
EST: gi|20300275|gb|BQ163218.1|BQ163218
EST:     CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT                         ACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
EST: gi|78088886|gb|DV517279.1|DV517279
EST:     CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT                         ACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
EST: gi|93284111|gb|EB676375.1|EB676375
EST:     CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT                         ACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
EST: gi|31406383|gb|CD485115.1|CD485115
EST:     CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT                         ACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
EST: gi|67010291|gb|CO439040.1|CO439040
EST:     CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT                         GCGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
EST: gi|18654801|gb|BM499606.1|BM499606
EST:     CTGGAAATCGATGACGACCAGAAACT                         ACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: CTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
EST: gi|31998590|gb|CD662145.1|CD662145
EST:     CCG-CTACCGGGTGCCAGAA-AAGCTGGAAATCGATGACGACCAGAAACT                         ACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
EST: gi|22935788|gb|BU572063.1|BU572063
EST:     CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT                         GCGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT
genomic: CCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCT

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: 49 (upstream exon), 49 (downstream exon)
Score: 2153

TTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCTGGGTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 975

TTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCTGGGTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 684

TTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCTGGGTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1040

TTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttc ... tcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCTGGGTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcttcatgctctacttgctttgatttctgataaacctttctatcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCTGGGTGAG
                           ttctgat  putative branch site (score: 1040)
                                     cctttctatc  putative PPT
                     tttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgcatccttttcttaacagagttattaaatcaaacatatgcttttttcttcatgctctacttgctttgatttctgataaacctttctatcaactatagACGTGCCTTTTATGACCGAAGGATCTCCCAGGAGGTCAGTGGTGATGCTCTGGGTGAG

- tgcatcc
- - - - - - - - - - - - - - - - -aaacata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttctga