RetrogeneDB ID: retro_ptro_1395

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 20:28005213..28005932(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: DKKL1
• Ensembl ID: ENSPTRG00000011292
• Aliases: None
• Description: dickkopf-like 1 [Source:HGNC Symbol;Acc:16528]

Sequence

>retro_ptro_1395
GAAACCTCCCTCACTCCCCCCGCAATGCGGCATCTGCTGGTCCTGCTGCTGCTCCTCTCTGCCCTGGTGACCTCCTTCAC
TGCAGCCTCTATCCACGATGCTCATGCCCAAGAGAGCTCCTTGGGTCTTACAGGCCTCCAGAGCCTACTCCAAGGCTTCA
GCCGACTTTTCCTGAAAGATGACCTGCTTCAGGGCATAGACATCTTCTTCTCTGCCCCCATGGACTTCCGGGGCCTCCCT
AGGAACTACCAACAAGAGGAGAACCAGGAGCACCAGCTGGGGAACAACACCCTCTCCAGCCACCTCCATATTGACAAGGT
GACCGACAATAAGACAGGAGAGGTGCTGATCTCCGAGAAGGTGGTGGCATCCATCCAGCCGGCGGAGGGGAGCTTCGAGG
GTAACTGGAAGGTACCCAGGATGGAGGAGGCGGCGGCCCTGGTGTCCATCCGGAAGGCTATGGACAACTTCCATGCAGAG
CTCCATCCCCGTGTGGCCTTCTGGATCATGAAGCTGCCACGGTGGAGGTCCCACCACAATGTCCTGGAGGGCGGCCGCTG
GCTCAGTGAGAAGCGACACCGCCTGCAGGCCATCCAGGATGGGCTCCACGAGGGGACCCGCGAGGACGTCCTAAAAGAGG
GGACCCAGGGCTCCTCCCACTCCGGGCTGTCCTCCGAAAGACCCACTTACTGTACATCCTCAGGTTCTCTTGGCAGCTA

Alignment

ORF - retro_ptro_1395 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.42 %
• Parental protein coverage: 99.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EASPPAPARRHLLVLLLLLSTLVIPSTAAPIHDADAQESSLGLTGLQSLLQGFSRLFLKGNLLRGIDSLF
          E.S...PA.RHLLVLLLLLS.LV...TAA.IHDA.AQESSLGLTGLQSLLQGFSRLFLK..LL.GID..F
Retrocopy ETSLTPPAMRHLLVLLLLLSALVTSFTAASIHDAHAQESSLGLTGLQSLLQGFSRLFLKDDLLQGIDIFF

Parental  SAPMDFRGLPGNYHKEENQEHQLGNNTLSSHLQIDKMTDNKTGEVLISENVVASIQPAERSFEGDLKVPR
          SAPMDFRGLP.NY..EENQEHQLGNNTLSSHL.IDK.TDNKTGEVLISE.VVASIQPAE.SFEG..KVPR
Retrocopy SAPMDFRGLPRNYQQEENQEHQLGNNTLSSHLHIDKVTDNKTGEVLISEKVVASIQPAEGSFEGNWKVPR

Parental  MEEKEALVPIQKATDSFHTELHPRVAFWIIKLPRRRSHQDALEGGHWLGEKRHRLQAIRDGLRKGTHKDV
          MEE..ALV.I.KA.D.FH.ELHPRVAFWI.KLPR.RSH...LEGG.WL.EKRHRLQAI.DGL..GT..DV
Retrocopy MEEAAALVSIRKAMDNFHAELHPRVAFWIMKLPRWRSHHNVLEGGRWLSEKRHRLQAIQDGLHEGTREDV

Parental  LEEGTESSSHSRLSP-RKTHLLYILRPSRQL
          L.EGT..SSHS.LS..RKTHLLYILR.S.QL
Retrocopy LKEGTQGSSHSGLSS<RKTHLLYILRFSWQL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.07 RPM
SRP007412_heart	0.00 RPM	0.17 RPM
SRP007412_kidney	0.00 RPM	0.13 RPM
SRP007412_liver	0.00 RPM	0.03 RPM
SRP007412_testis	0.00 RPM	135.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1395 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1395 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1395 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2421

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000102	1 retrocopy	retro_cjac_1433,
Homo sapiens	ENSG00000104901	1 retrocopy	retro_hsap_2421,
Gorilla gorilla	ENSGGOG00000016382	1 retrocopy	retro_ggor_1506,
Macaca mulatta	ENSMMUG00000014794	1 retrocopy	retro_mmul_627,
Pan troglodytes	ENSPTRG00000011292	1 retrocopy	retro_ptro_1395 ,