RetrogeneDB ID: retro_ptro_2643

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:99539882..99541275(-)
• Located in intron of: ENSPTRG00000019442

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF14
• Ensembl ID: ENSPTRG00000017356
• Aliases: None
• Description: None

Sequence

>retro_ptro_2643
ATGTTGTCAGAAGACTGAGAAGCTCAGGAGGTGAGCTGCTGGCCCTGGCGAGTATTTAAGATGGAGATGAATTCGGAAAA
GCAAAGCCTGTCCGAGGTGGAGAAATCAGCATCGATCGGGATTTGCCACAGAACTTCAAGTTATTTGTGAGTGGCAATTC
AGATGAGTGCCCCCAGAATAGTAGCTTTGAATATACCATTTGCTTTCTCCCTCCACTTGTGCTGAACTCTGAACTGCCAC
CAGATTATCCATCCTCCTTCCCACCTTCATTCACACTTAGTGGCAAATTGCCGTCACCAACTCAGCTCTCTGCTCTATGC
AAGCACTTAGACAACCTATGGGAAGAACACAGTGGCAGTGGGATCCTGTCTGCCTGGATGCAGTTTCTTAAGCAAGAGAC
CCTGGTGCACCCCAATATTGTCTCTCCCTCTGAGCTCACGATGGGTTCTCAGGAAAAAGTGCCGAGAAGGATAGCGCAAG
CCCCTCCCATCAGAGCTAGATTTTGGAGGAGCTGCTGGATCTCATGTAGATCAAGAGGAAATTGTGGATGAGAGAGCTGT
GCAGGATGTGGAATCACTGTCAAGTCTGATCCAGGAAATCTTGGACTTTCATCAAGCTTAGCAGATAAAATGCTTTAATA
GTAGATTGTTCCTGTACAACATCTGTTTCTGCGAGAAGCTGGGCAGTGAATGCATGTACCTCTTGGAGTGAGGCCTGTGT
ACTGCAAAGCCTATCTGAAGGACTGCTTTGAAATCCAGATCAGAGATGGCCAGGTTCAATGCCTCAACTGCTCAGAACCA
AAGTGCCCTTCGGTGGCCACTCCTGGCCAGGTCAAAGAGCCAGCGGAAGCAGAGTTCTCTGCCTGTCATGGCTGCCTTCT
CCTCCCATCCACCTTGGAGCTAGTGGCAGATGTGGTGTGCTGCCCCCGCCTGTGGGGGCTTGCAGGGCCTGGCTGTACCA
CGGGCATCTGCTCCAGCTGTAACTTTGCCTTCTGTACCTTGTGCAGACTGACCTACCATGGGGCCTCTCCATGTAAGGTG
ATGGCAGAGAAATTAACAGACTTACAAAACGAATACCTGCAAGCAGATGAGGCCAAGACAAGATTTCTGGAACAGAGGTA
AGGTAAGAGGGTGAGTCAGAGGGCACTGGAAGAGATGGAAAGTAAGGAGTGGCTAGAAGAGAACTCGAAGAGATGCCCAT
GCTGTGGAATTCACATAGAGAAGTGAGGTGGATGCCATGTACTGGCTGCAGGCTCTATTTCTATTGGGTCGGCATGGGTT
CTCTCTCTAGCAACCCCTTACAAACATTTCGCCAACCCTACTTCACCGTGTTGTAACCGGCTGTTTCATGCTTGGATATG
AATGGAGACATTGGGGAAGATGAGATTGAAGAC

Alignment

ORF - retro_ptro_2643 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.59 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSSEDREAQE-DELLALASIYDGDEFRKAESVQGGETRIYLDLPQNFKIFVSGNSNECLQNSGFEYTICF
          M.SED.EAQE..ELLALASI.DGDEF.KA..V.GGE..I..DLPQNFK.FVSGNS.EC.QNS.FEYTICF
Retrocopy MLSED*EAQE<GELLALASI*DGDEFGKAKPVRGGEISIDRDLPQNFKLFVSGNSDECPQNSSFEYTICF

Parental  LPPLVLNFELPPDYPSSSPPSFTLSGKWLSPTQLSALCKHLDNLWEEHRGSVVLFAWMQFLKEETLAYLN
          LPPLVLN.ELPPDYPSS.PPSFTLSGK..SPTQLSALCKHLDNLWEEH.GS..L.AWMQFLK.ETL...N
Retrocopy LPPLVLNSELPPDYPSSFPPSFTLSGKLPSPTQLSALCKHLDNLWEEHSGSGILSAWMQFLKQETLVHPN

Parental  IVSPFELKIGSQ-KKVQRRTAQASPNTELDFGGAAGSDVDQEEIVDERAVQDVESLSNLIQEILDFDQAQ
          IVSP.EL..GSQ.KK.........P..ELDFGGAAGS.VDQEEIVDERAVQDVESLS.LIQEILDF.QA.
Retrocopy IVSPSELTMGSQ>KKCREG*RKPLPS-ELDFGGAAGSHVDQEEIVDERAVQDVESLSSLIQEILDFHQA*

Parental  QIKCFNSKLFLCNICFCEKLGSECMYFLE-CRHVYCKACLKDYFEIQIRDGQVQCLNCPEPKCPSVATPG
          QIKCFNS.LFL.NICFCEKLGSECMY.LE..R.VYCKA.LKD.FEIQIRDGQVQCLNC.EPKCPSVATPG
Retrocopy QIKCFNSRLFLYNICFCEKLGSECMYLLE<VRPVYCKAYLKDCFEIQIRDGQVQCLNCSEPKCPSVATPG

Parental  QVKELVEAELFARYDRLLLQSSLDLMADVVYCPRPCCQLPVMQEPGCTMGICSSCNFAFCTLCRLTYHGV
          QVKE..EAE..A....LLL.S.L.L.AD.V.C...C..L.....PGCT.GICSSCNFAFCTLCRLTYHG.
Retrocopy QVKEPAEAEFSACHGCLLLPSTLELVAD-VVC---CPRLWGLAGPGCTTGICSSCNFAFCTLCRLTYHGA

Parental  SPCKVTAEKLMDLRNEYLQADEANKRLLDQRYGKRVIQKALEEMESKEWLEKNSKSCPCCGTPIEKLDGC
          SPCKV.AEKL.DL.NEYLQADEA..R.L.QR.GKRV.Q.ALEEMESKEWLE.NSK.CPCCG..IEK..GC
Retrocopy SPCKVMAEKLTDLQNEYLQADEAKTRFLEQR*GKRVSQRALEEMESKEWLEENSKRCPCCGIHIEK*GGC

Parental  NKMTCTGCMQYFCWICMGSLSRANPYKHFNDPGSPCFNRLFYA-VDVDDDIWEDEVED
          .............W.....LS.A.PYKHF..P.SPC.NRLF.A..D...DI.EDE.ED
Retrocopy HVLAAGSISIGSAWV----LSLATPYKHFANPTSPCCNRLFHA<LDMNGDIGEDEIED

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	0.20 RPM	38.91 RPM
SRP007412_cerebellum	0.65 RPM	45.74 RPM
SRP007412_heart	0.03 RPM	43.11 RPM
SRP007412_kidney	0.24 RPM	55.00 RPM
SRP007412_liver	0.10 RPM	23.04 RPM
SRP007412_testis	0.21 RPM	74.72 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2643 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2643 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2643 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3881
Gorilla gorilla	retro_ggor_2612
Pongo abelii	retro_pabe_3115

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000007803	1 retrocopy	retro_dnov_332,
Dasypus novemcinctus	ENSDNOG00000024423	1 retrocopy	retro_dnov_1704,
Homo sapiens	ENSG00000013561	2 retrocopies	retro_hsap_3790, retro_hsap_3881,
Gorilla gorilla	ENSGGOG00000008542	1 retrocopy	retro_ggor_2612,
Macaca mulatta	ENSMMUG00000009768	2 retrocopies	retro_mmul_1647, retro_mmul_934,
Pongo abelii	ENSPPYG00000015894	2 retrocopies	retro_pabe_3095, retro_pabe_3115,
Pan troglodytes	ENSPTRG00000017356	2 retrocopies	retro_ptro_2571, retro_ptro_2643 ,