RetrogeneDB ID: retro_ptro_3090

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:9304996..9306094(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDYL
• Ensembl ID: ENSPTRG00000017688
• Aliases: None
• Description: chromodomain protein, Y-like [Source:HGNC Symbol;Acc:1811]

Sequence

>retro_ptro_3090
ATTGAAAAGATTGTTGACAAAAGGAAAAATTAAAAAGGGAAGAGAGAGTATTTGGTTCAGTGAAAAGGCTACAACAGCGA
GGACAACACTTGGGAACCAGAGCAGCACCTCGTGAACTGTCAGGAATACATCCACGACTTCAACAGACACCACACGGAAA
GGCAGAAAGAGAGCACATTGACCAGAACAAACAGGTCCTCTCCCAACAATGCTAGGAAACAAATCTCCAGATCCACAAAC
AGCAGCTTTTCTAAGTCCTCTCCTAAGGCACCAGTGATTGGGAGAGATCACGAATCCAAAAACAGCCAGCTGTTTGCTGC
CAGCCAGCAGTTCAGGAAGAACACAGCTCCGTCTCTCTGCAGCCAGATGAAAATGGACCTAGTGAAGTCAGGTATCAAGA
TCCTCATGCCTAAGAGCCCCATTAAGCAGGACGCAGTGAATGGCTTTCAGAGTGAGAGCCCCAAAAAACTGGACCCCACA
GAGCAGGGTCAGGAGGAATGGTAGTACCCAAAGTGGCAGCAGAAAAGCCAGACAAAGCTTTATTGGGCCATGGTGCTGAG
TAGGCCAGGATGGGGAGCAAGCCTGGATACACCTGCTAGTGCTCAGGGTGCATGGCCCCATAAGTGCAGCCATGGCCACA
GGCTTACTCGTTAACAGGAAAGCTACATCTACATTCATAGATGCATTAACAGCCAGTGGGACAAGCAACATACAGACATC
TGTTACAGGAGTAACTGTCAGCAAAAGGAAATTTATTGACAACAGAAGAGAACAGCCTTTTAACAAACGATTGCATTTCA
GTGTGAGGCAAACAGAAAGGGCCTACGGATACAGAGTTATTGTGGTCGGGACAAAAGATGGCTTCACCCACATCTTATTC
ACTAGATCAACAGGGAATAACTCAGTAAATACAGCTGTAATGAAAAAAGTCTACCAGCTCTGACAACCACTGCTGATTAC
AACAAGCTTGTACTGCTCAGCGCCTTTAACAGTGTCTTCTGTTGTGGACTTGACTTTATTTATTTTATGCAGTGTTTGAC
AGATGACAGAAAAAGAGAAAGGATTAAAATGGGAGAACCTATCAGAAACGTCGTGAAT

Alignment

ORF - retro_ptro_3090 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.53 %
• Parental protein coverage: 61.87 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VERIVDKRKNKKGKTEYLVRWKGYDSDDDTWEPEQHLVNCEEYIHDFNRRHTEKQKESTLTRTNRTSPNN
          .E.IVDKRKN.KGK.EYLV..KGY.S.D.TWEPEQHLVNC.EYIHDFNR.HTE.QKESTLTRTNR.SPNN
Retrocopy IEKIVDKRKN*KGKREYLVQ*KGYNSEDNTWEPEQHLVNCQEYIHDFNRHHTERQKESTLTRTNRSSPNN

Parental  ARKQISRSTNSNFSKTSPKALVIGKDHESKNSQLFAASQKFRKNTAPSLSSRKNMDLAKSGIKILVPKSP
          ARKQISRSTNS.FSK.SPKA.VIG.DHESKNSQLFAASQ.FRKNTAPSL.S...MDL.KSGIKIL.PKSP
Retrocopy ARKQISRSTNSSFSKSSPKAPVIGRDHESKNSQLFAASQQFRKNTAPSLCSQMKMDLVKSGIKILMPKSP

Parental  VKSRTAVDGFQSESPEKLDPVEQGQED-TVAPEVAAEKPVGALLGPGAERARMGSRPR-IHPLVPQVPGP
          .K...AV.GFQSESP.KLDP.EQGQE...V.P.VAAEKP..ALLG.GAE.ARMGS.P..IH.LV..V.GP
Retrocopy IK-QDAVNGFQSESPKKLDPTEQGQEE<MVVPKVAAEKPDKALLGHGAE*ARMGSKPG<IHLLVLRVHGP

Parental  VTAAMATGLAVNGKGTSPFMDALTANGTTNIQTSVTGVTASKRKFIDDRRDQPFDKRLRFSVRQTESAYR
          ..AAMATGL.VN.K.TS.F.DALTA.GT.NIQTSVTGVT.SKRKFID.RR.QPF.KRL.FSVRQTE.AY.
Retrocopy ISAAMATGLLVNRKATSTFIDALTASGTSNIQTSVTGVTVSKRKFIDNRREQPFNKRLHFSVRQTERAYG

Parental  YRDIVVRKQDGFTHILLSTKSSENNSLNPEVMREVQS-ALSTAAADDSKLVLLSAVGSVFCCGLDFIYFI
          YR.IVV...DGFTHIL..T.S..NNS.N..VM..V...AL.T..AD..KLVLLSA..SVFCCGLDFIYF.
Retrocopy YRVIVVGTKDGFTHILF-TRSTGNNSVNTAVMKKVYQ<ALTT-TADYNKLVLLSAFNSVFCCGLDFIYFM

Parental  RRLTDDRKRESTKMAEAIRNFVN
          ..LTDDRKRE..KM.E.IRN.VN
Retrocopy QCLTDDRKRERIKMGEPIRNVVN

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	0.11 RPM	6.92 RPM
SRP007412_cerebellum	0.00 RPM	13.41 RPM
SRP007412_heart	0.00 RPM	12.71 RPM
SRP007412_kidney	0.00 RPM	14.98 RPM
SRP007412_liver	0.00 RPM	14.34 RPM
SRP007412_testis	0.53 RPM	21.92 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3090 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3090 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3090 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4651

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011787	1 retrocopy	retro_chof_525,
Callithrix jacchus	ENSCJAG00000021374	5 retrocopies	retro_cjac_2675, retro_cjac_3927, retro_cjac_4003, retro_cjac_4228, retro_cjac_4229,
Homo sapiens	ENSG00000153046	1 retrocopy	retro_hsap_4651,
Otolemur garnettii	ENSOGAG00000015920	2 retrocopies	retro_ogar_2406, retro_ogar_3269,
Pan troglodytes	ENSPTRG00000017688	1 retrocopy	retro_ptro_3090 ,
Pan troglodytes	ENSPTRG00000021099	1 retrocopy	retro_ptro_1612,