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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcctaatcggaagcagaatttacttaataatccaggttcctgttttcatgttctcttttgcatgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG

Basic information

species Zea mays
transcript GRMZM5G836910_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G836910_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g55420.1 (Oryza sativa), 3'ss of exon 3
gtgagcctaatcggaagcagaatttacttaata-atccaggttcctgttttcatgttct-cttttgcatgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
|| || |||||   |   |  |||| ||||||| | |   |||| |||| | |    ||  | || || ||  ||  |||||||| ||||||||||||||||||||||||||| |||
gtaagtctaataatacctatcatttccttaatataactcagttcttgttgtgacacactattcttacacgtggta--gGCTGAAACTCTTATGTTGGAGAAAGGAGAAAACAAGGAG

upper sequence: GRMZM5G836910_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0008g06040.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------------------------------------gtgagcctaatcggaagcagaattta-----cttaataatccaggttcctgttttcatgttctcttttgcatgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
                                                            | |||||  |  |||    |  |||      ||| |  | |   |||||| | | ||      ||       || | ||||| |||||||||||| |||||| ||||||||| ||||||
gtcagttttcttttttagaacttaatcatcactaactgatccataaataggattattttttaagccttttatgaatataatcttaatgcttttacttctacttcttcctgatataatagatcgttggtttcattttctagGCAGAAAATCTTATGCTGGAGAGAGGAGAAAATAAAGAG
















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|211140316|gb|FL028761.1|FL028761
EST:     CCTATAGGACAGAAGAGCTGCAGCCATACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
EST: gi|211235881|gb|FL028766.1|FL028766
EST:     CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATG
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATG
EST: gi|211240363|gb|FL028799.1|FL028799
EST:     CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGTATCTTCCCA
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGTATCTTCCCA
EST: gi|94477439|gb|EB706397.1|EB706397
EST:     CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
EST: gi|71440750|gb|DR821800.1|DR821800
EST:     CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
EST: gi|211235892|gb|FL028777.1|FL028777
EST:     CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGTATCTTCCCA
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGTATCTTCCCA
EST: gi|211240361|gb|FL028797.1|FL028797
EST:     CCTATAGGACAGAAGAGCTGCAGCCATACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
EST: gi|149107658|gb|EE189537.2|EE189537
EST:     CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
EST: gi|211235886|gb|FL028771.1|FL028771
EST:     CCTATAGGACAGAAGAGCTGCAGCCATACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
EST: gi|211140315|gb|FL028760.1|FL028760
EST:     CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
EST: gi|211238128|gb|FL028788.1|FL028788
EST:     CCTATAGGACAGAAGAGCTGCAGCCATACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATG
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATG
EST: gi|78104308|gb|DV522726.1|DV522726
EST:     CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
EST: gi|211235895|gb|FL028780.1|FL028780
EST:     CCTATAGGACAGAAGAGCTGCAGCCATACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATGTTGGAGAAAAGGAGAAAAC
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAA-GGAGAAAAC
EST: gi|76289791|gb|DV029359.1|DV029359
EST:     CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
EST: gi|211140308|gb|FL028753.1|FL028753
EST:     CCTATAGGACAGAAGAGCTGCAGCCATACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
EST: gi|148941508|gb|EC886438.2|EC886438
EST:     CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
EST: gi|211140313|gb|FL028758.1|FL028758
EST:     CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
EST: gi|211240365|gb|FL028801.1|FL028801
EST:     CCTATAGGACAGAAGAGCTGCAGCCATACGTGCTCAATGTAGTCAAGAAG                         GGTGAAAATCTTATGTTGGAGAAAGGAGACAACAAAGAG
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
EST: gi|78114229|gb|DV532618.1|DV532618
EST:     CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
EST: gi|211240360|gb|FL028796.1|FL028796
EST:     CCTATAGGACAGAAGAGCTGCAGCCATACGTGCTCAATGTAGTCAAAAAG                         GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
EST: gi|211140314|gb|FL028759.1|FL028759
EST:     CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGTATCTT
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGTATCTT
EST: gi|211235884|gb|FL028769.1|FL028769
EST:     CCTATAGGACAGAAGAGCTGCAGCCATACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
EST: gi|149000841|gb|EE038069.2|EE038069
EST:     CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
EST: gi|211240366|gb|FL028802.1|FL028802
EST:     CCTATAGGACAGAAGAGCTGCAGCCATACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGTATCTTC
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAGTATCTTC
EST: gi|211139377|gb|FL028748.1|FL028748
EST:     CCTATAGGACAGAAGAGCTGCAGCCATACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
EST: gi|211235891|gb|FL028776.1|FL028776
EST:     CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATGTT
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTT
EST: gi|211140317|gb|FL028762.1|FL028762
EST:     CCTATAGGACAGAAGAGCTGCAGCCATACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
EST: gi|211238126|gb|FL028786.1|FL028786
EST:     CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
EST: gi|71767561|gb|DR965498.1|DR965498
EST:     CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
EST: gi|211139376|gb|FL028747.1|FL028747
EST:     CCTATAGGACAGAAGAGCTGCAGCCATACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
EST: gi|211238131|gb|FL028791.1|FL028791
EST:     CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAG                         GCTGAAAATCTTATGT
genomic: CCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGT

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), 39 (downstream exon)
Score: 68

GGCCTTTAAAGCAGATAAAAGCGAGCTGAAGCTCAATCTTGGTGTTGGTGCCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 423

GGCCTTTAAAGCAGATAAAAGCGAGCTGAAGCTCAATCTTGGTGTTGGTGCCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 73

GGCCTTTAAAGCAGATAAAAGCGAGCTGAAGCTCAATCTTGGTGTTGGTGCCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG


Block sizes: 48 (upstream exon), 39 (downstream exon)
Score: 334

GGCCTTTAAAGCAGATAAAAGCGAGCTGAAGCTCAATCTTGGTGTTGGTGCCTATAGGACAGAAGAGCTGCAGCCCTACGTGCTCAATGTAGTCAAGAAGgtgagcctaa ... tgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttacttaataatccaggttcctgttttcatgttctcttttgcatgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG
    acttaat  putative branch site (score: 334)
                                            atgttatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcctaatcggaagcagaatttacttaataatccaggttcctgttttcatgttctcttttgcatgttatatagGCTGAAAATCTTATGTTGGAGAAAGGAGAAAACAAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA