RetrogeneDB ID: retro_ptro_2784

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:100160406..100161114(-)
• Located in intron of: ENSPTRG00000020480

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDCL2
• Ensembl ID: ENSPTRG00000016073
• Aliases: None
• Description: phosducin-like 2 [Source:HGNC Symbol;Acc:29524]

Sequence

>retro_ptro_2784
ATGCAGGACCCCAACACAGACACTGAGTGGAATGACATCTTAGACAAGAATGGCATCTTACCCACCAAGGAAAGTCTAAA
AGAATCAGAAGAGAAGGCAGAAGAGGAGCAGCATATCCTTCAGCAGTCAGTGGTGACAACATACGAAGATATGACTTTGG
AAGAGCTGGAGGATCATGAAGACGAGTTTAATGAGGAGGATGAACATGCTATTGAAATGTACAGATGGCAGAGACTCGCT
GAGGGGAAAGCAATTAAACTGAAGAATAAATTTGGAGAAGTTTTGGAGATTTCAGGGAAGTATTATGTTCAAGAAGTTAC
CAAAGCCAGTGAGGGCTTGTGGGTCATCTTGCACCTTTGCAAACAAGGAATTCCCCTCTGTGCCCTGATAAATCAGCACC
TCAGTGGACTTGCCAGGAAGTTTCCTGATGTCAAATTTATCAAAGCCAATTCAACCACCTGCATACCCAATTATCCTGAT
AGGAATCTGCCCATGATATTTGTTTACTTGGAAGGAGACATCAAGGCTCAGTTGATCGGTCCTCTGGTGTTTGGCGGCAT
GAACCTGACCAGAGATGAGTTGGGGTGGAAACTGTCTGAATCTGGAGCAGTTAAGACGGACTTGGAGGAAAACCCTAAGA
AGCCGATTGAAGGTGTGTTGCTGTCTTCAGTGCAGAGCTCTGTCCCCATGAGGAGGGACAGCGATTCC

Alignment

ORF - retro_ptro_2784 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.24 %
• Parental protein coverage: 96.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQDPNEDTEWNDILRDFGILPPKEESKDEIE--EMVLRLQKEAMVKPFEKMTLAQLKEAEDEFDEEDMQA
          MQDPN.DTEWNDIL...GILP.KE..K...E..E..........V...E.MTL..L...EDEF.EED..A
Retrocopy MQDPNTDTEWNDILDKNGILPTKESLKESEEKAEEEQHILQQSVVTTYEDMTLEELEDHEDEFNEEDEHA

Parental  IETYRKKRLQEWKALKKKQKFGELREISGNQYVNEVTNAEEDVWVITHLYRSSIPMCLLVNQHLSLLARK
          IE.YR..RL.E.KA.K.K.KFGE..EISG..YV.EVT.A.E..WVI.HL....IP.C.L.NQHLS.LARK
Retrocopy IEMYRWQRLAEGKAIKLKNKFGEVLEISGKYYVQEVTKASEGLWVILHLCKQGIPLCALINQHLSGLARK

Parental  FPETKFVKAIVNSCIQHYHDNCLPTIFVYKNGQIEAKFIGIIECGGINLKLEELEWKLAEVGAIQTDLEE
          FP..KF.KA....CI..Y.D..LP.IFVY..G.I.A..IG....GG.NL...EL.WKL.E.GA..TDLEE
Retrocopy FPDVKFIKANSTTCIPNYPDRNLPMIFVYLEGDIKAQLIGPLVFGGMNLTRDELGWKLSESGAVKTDLEE

Parental  NPRKDIVDMMVSSIRNT-SIHDDSDS
          NP.K.I.....SS.........DSDS
Retrocopy NPKKPIEGVLLSSVQSSVPMRRDSDS

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	0.09 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.09 RPM	0.06 RPM
SRP007412_kidney	0.21 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.21 RPM	45.53 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2784 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2784 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2784 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4102
Callithrix jacchus	retro_cjac_1486

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012692	3 retrocopies	retro_chof_1554, retro_chof_562, retro_chof_737,
Echinops telfairi	ENSETEG00000000666	1 retrocopy	retro_etel_1568,
Gorilla gorilla	ENSGGOG00000007908	1 retrocopy	retro_ggor_2890,
Monodelphis domestica	ENSMODG00000020680	2 retrocopies	retro_mdom_1048, retro_mdom_993,
Pan troglodytes	ENSPTRG00000016073	7 retrocopies	retro_ptro_148, retro_ptro_1810, retro_ptro_1865, retro_ptro_2402, retro_ptro_2690, retro_ptro_2784 , retro_ptro_675,