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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcagccctgtagtttcctatcttgcaaaggagcagtgcctttctcaaactttgctgatgagagattattttgtgattactgtgttctttactgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAG

Basic information

species Zea mays
transcript GRMZM2G177273_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177273_T01 (Zea mays), 3'ss of exon 6
lower sequence: 13113.m00157 (Oryza sativa), 3'ss of exon 7
---gtcagccctgtagtttcctatcttgcaaaggagcagtgcctttctcaaactttgctgatgagagattattttgtgattactgtgttctttactgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAG
   |     ||| | |||||   | |   |         |||| || ||  | ||   |      |||||||| | |||| |   |||    |||  |||||||||||||||||||||||||| ||||||||||||||||| |||||||| ||||||| ||| || || || |||||||| ||||||||||||
atggattttcctatcgtttctagtttgatatta---tcttgcccttttcggatttcagttcccgaagattattgtttgataataatgtatgctaccaatgcagACTAGTTATTCATACCTTGATGTTGTTGGAAGGACGACAGTTGTACTAAAGAAGAGAAACGTAGTTGGAGAGCACAATGTTCCTTTCCAG

upper sequence: GRMZM2G177273_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv13s0019g04410.t01 (Vitis vinifera), 3'ss of exon 6
gtcagccctgtagtttcctatcttgcaaaggagcagtgc-ctttctcaaactttgctgatgagagat-tattttg--tgattactgtgttctttactgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAG
  ||  | | |  |  | ||    |   | |     |   |  |  ||  ||  ||   |  | | | ||| ||   ||| |  | |  | |  |    ||||||| |||||||| |||||||| ||||||||||||||   ||| || ||  | ||||||||||| ||    |||||||   |||||||||||
--cattctttt--tcccttagtaagtgcatggattatatgcacttgcagcctcagcattttggtggtatatgttaactgaatcttttcgtttgaatctgtgcagACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAG
















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|78024949|gb|DV493336.1|DV493336
EST:     CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAG                         ACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
genomic: CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
EST: gi|32930107|gb|CF034919.1|CF034919
EST:     CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAG                         ACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACAGTTGTA
genomic: CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTA
EST: gi|6654207|gb|AW267612.1|AW267612
EST:     CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAG                         ACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
genomic: CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
EST: gi|5455857|gb|AI833547.1|AI833547
EST:     CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAG                         ACTAGTTATTCATACCTTGACGTTGTTGGAAGGGCGACGGTTGTACTGAAG
genomic: CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
EST: gi|32932468|gb|CF037280.1|CF037280
EST:     CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAG                         ACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTAC
genomic: CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTAC
EST: gi|166703330|gb|EG124319.1|EG124319
EST:     AGAAACATCTTGAG                         ACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
genomic: AGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
EST: gi|211408847|gb|FL082357.1|FL082357
EST:     CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAG                         ACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
genomic: CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
EST: gi|37387875|gb|CF631140.1|CF631140
EST:     GTGACAGAGAAACATCTTGAG                         ACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
genomic: GTGACAGAGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
EST: gi|78023626|gb|DV492013.1|DV492013
EST:     CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAG                         ACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
genomic: CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
EST: gi|22542436|gb|BU092874.1|BU092874
EST:     CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAG                         ACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
genomic: CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
EST: gi|5468696|gb|AI834487.1|AI834487
EST:     CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAG                         ACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
genomic: CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
EST: gi|17921687|gb|BM259338.1|BM259338
EST:     CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAG                         ACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
genomic: CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
EST: gi|33093879|gb|CF053873.1|CF053873
EST:     CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAG                         ACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTAC
genomic: CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTAC
EST: gi|78075801|gb|DV504235.1|DV504235
EST:     CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAG                         ACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
genomic: CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
EST: gi|33093279|gb|CF053273.1|CF053273
EST:     CAAAAAATCCAGAGCGTGTAGTTCCTTTTGTGACAGAGAAACATCTTGAG                         ACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGT
genomic: CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGT
EST: gi|20803243|gb|BQ294293.1|BQ294293
EST:     CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAG                         ACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
genomic: CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
EST: gi|32932488|gb|CF037300.1|CF037300
EST:     CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAG                         ACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTAC
genomic: CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTAC
EST: gi|12969533|gb|BG266477.1|BG266477
EST:     CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAG                         ACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGA
genomic: CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGA
EST: gi|21331859|gb|BQ487240.1|BQ487240
EST:     CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAG                         ACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
genomic: CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
EST: gi|71763848|gb|DR961785.1|DR961785
EST:     CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAG                         ACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
genomic: CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
EST: gi|23199481|gb|BU582046.1|BU582046
EST:     CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAG                         ACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
genomic: CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
EST: gi|5069740|gb|AI737705.1|AI737705
EST:     CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAG                         ACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
genomic: CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
EST: gi|74236700|gb|DT644614.1|DT644614
EST:     CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAG                         ACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
genomic: CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
EST: gi|60397407|gb|DN230223.1|DN230223
EST:     CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAG                         ACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
genomic: CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
EST: gi|60352174|gb|DN219147.1|DN219147
EST:     CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAG                         ACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG
genomic: CAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAG

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: 48 (upstream exon), 45 (downstream exon)
Score: 461

GTTGTGCTTCCTGAAGGATCAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 309

GTTGTGCTTCCTGAAGGATCAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 239

GTTGTGCTTCCTGAAGGATCAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 356

GTTGTGCTTCCTGAAGGATCAAAAAATCCAGAGCATGTAGTTCCTTTTGTGACAGAGAAACATCTTGAGgtaattccat ... actgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaactttgctgatgagagattattttgtgattactgtgttctttactgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAG
                                            tactgat  putative branch site (score: 356)
                                       ttctttact  CT-rich tract
                   attattttgtgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagccctgtagtttcctatcttgcaaaggagcagtgcctttctcaaactttgctgatgagagattattttgtgattactgtgttctttactgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - -ccctgta
- - - - - - - - - - tcttgca
- - - - - - - - - - - - - - -ggagcag
- - - - - - - - - - - - - - - - - - tgccttt
- - - - - - - - - - - - - - - - - - - - - - - - - - -gctgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgatt