RetrogeneDB ID: retro_ptro_941

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:87413197..87414882(+)
• Located in intron of: ENSPTRG00000006602

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM35A
• Ensembl ID: ENSPTRG00000002465
• Aliases: None
• Description: family with sequence similarity 35, member A [Source:HGNC Symbol;Acc:28773]

Sequence

>retro_ptro_941
GTACATTCTGTTTCTGAAACACAGAATATAGAATCCCAGAAGATTCACTCCTCTAGACTGAGTGAGGTAACGAGCTCTAA
TATGCAAATATGTGGATTTGAAAGCATAGTTCTGCATTTAACTGAAAAGTATCAAAAGCTTCTCAGTGAAAATAAAATGA
TAGATGAACAGCCTAAACATCAGTCAGATATATGTGGTCAGAACTTTCACTCAAATTTGTTTCAGTTAGGCCACAAATGT
GCAGCTATGTTGGATTTGGTTTGTAGTACTAAACAAATTAATATAGGGCCTGAAGTGGTATAAAGAGAGTGTGTGCCAAC
AGAATATCATGAAATACAAAATCAGTGTTTGCGATTATTTTCCTTGAACACAGTAGATAAGCCAAGGTCTGAAGCAGCAG
TTAGGAAGGTCTCAGACCTTAAAATGTCAACTGATACGGAATTTCTCTGTATAATTACCTCCAGCCAGGTTGCTTTTTTA
GCTCAAAAGAAAGATAAAGGGCGGAGTCCTATAAATAAAGGGAATGTAAACATGGAGACTGAACCAAAGGCAAGTTACGG
GAAGATAAGAATATCTGAAGAGAATTCCATTCAACTTGATGATTTTACAGAAGCATATGAAAGTGGACAAAACCAAGCAT
ATTCTCTTGAACATTTTAGTCCTGTTTGTCCTAAAACAGAAAATAGCCACATTCACATAAACTCTGACAAAGGTCCTGAA
GAAAATACAGGATCTCAAGAACTTTTCAGTTCTGAAGATGAACTGCCACCAAATGAGATACGTATTGAGTTGTGTAGCTC
AGGAATACTGTGTTCCCAACTAAACACCTTCCACAAAAGTGCTATTAAAAGAAGCTGCACCTCTGAAGATAAAGTGGGCC
AGTCTGAAGTTCTATCTAGAGTCCTTCAAGTAGCTAAGAAAATGAAGTTGATTTCTAATGCAGGAGATTCTGTTGTAGAA
ATGGATCAGAGGAATGTGTCTGAATTTAAGGGTATTTTAAAAAGTCATTAATAAAAAACTGTGATTCTAAAAGCCAGAAG
TATGATTGTTTAGTCATGGTGCTATCTCCATGTCACGTGAAGGAAATAAACATAAAATTCGGACCAAATTCTGGCCCTAA
AGTGCCTTTAGCAACAGTTACAGTAATTGATCAATCAGAAACTAAGAAGGTTTTTCTGTAGAGGACTGCAGCATTTTGGG
CATATACAGTGTTTCTTGGAGATATAATTTTACTCGCAGATGTTGTTATTCATGAGGACCAATGGGTTGGCGAGACAGTA
CTACAATCAACATTTAGCAGTCAGTTATTAAATCTTGGGAGTTATTCATCTATTCAGCCTGAAGAATATTCCAGTGTAGT
TAGTGATGTTGTACTTCAAGACCTACTGGCACATGTGTCCTCAAAACATTCCTACCTCAGAGATCTTCCTCCGAGGCAGC
CTCAGAGGGTGAACAGTATAGACTTTATAGAATTGGAGCACCTTCAGCCTGATGTATTAGTCCACACAATACTAAGAGTT
GTTGATTTCACTATACTGACAGAGGCAGTATACAGTTATAGAGGACAGAAGCAGAAAAAAGTTATGTTAACAGTGGAACA
GGCCCAAGATCAACATTATGTGCTTGTATTATGGAGTCCTGGAGCAGCCTGGTACCCTCAACTTCAAAGGAAAAAAGGTT
ATATT

Alignment

ORF - retro_ptro_941 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.11 %
• Parental protein coverage: 67.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VHSVSETQNIESQKIHSSRLSDITSSNMQICGFKSTVPHLTEEEKYQKLLSENKMRDEQPKHQPDICGKN
          VHSVSETQNIESQKIHSSRLS..TSSNMQICGF.S.V.HLTE..KYQKLLSENKM.DEQPKHQ.DICG.N
Retrocopy VHSVSETQNIESQKIHSSRLSEVTSSNMQICGFESIVLHLTE--KYQKLLSENKMIDEQPKHQSDICGQN

Parental  FNTNLFQLGHKCAAVLDLVCSTEKINIGPEVVQRECVPTEYHEIQNQCLGLFSSNAVDKSRSEAAVRKVS
          F..NLFQLGHKCAA.LDLVCST..INIGPEVV.RECVPTEYHEIQNQCL.LFS.N.VDK.RSEAAVRKVS
Retrocopy FHSNLFQLGHKCAAMLDLVCSTKQINIGPEVV*RECVPTEYHEIQNQCLRLFSLNTVDKPRSEAAVRKVS

Parental  DLKISTDTEFLSIITSSQVAFLAQKKDKRRSPVNKGNVNMETEPKASYGEIRIPEENSIQLDGFTEAYES
          DLK.STDTEFL.IITSSQVAFLAQKKDK.RSP.NKGNVNMETEPKASYG.IRI.EENSIQLD.FTEAYES
Retrocopy DLKMSTDTEFLCIITSSQVAFLAQKKDKGRSPINKGNVNMETEPKASYGKIRISEENSIQLDDFTEAYES

Parental  GQNQAYSLELFSPLCPKTENSRIHINSDKGLEEHTGSQELFSSEDELPPNEIRIELCSSGILCSQLNTFH
          GQNQAYSLE.FSP.CPKTENS.IHINSDKG.EE.TGSQELFSSEDELPPNEIRIELCSSGILCSQLNTFH
Retrocopy GQNQAYSLEHFSPVCPKTENSHIHINSDKGPEENTGSQELFSSEDELPPNEIRIELCSSGILCSQLNTFH

Parental  KSAIKRSCTSDDKVGQSEALSRVLQVAKKMKLISNGGDSAVEMDRRNVSEFKNIKKT-SLIKNCDSKSQK
          KSAIKRSCTS.DKVGQSE.LSRVLQVAKKMKLISN.GDS.VEMD.RNVSEFK.I.K..SLIKNCDSKSQK
Retrocopy KSAIKRSCTSEDKVGQSEVLSRVLQVAKKMKLISNAGDSVVEMDQRNVSEFKGILKS<SLIKNCDSKSQK

Parental  YNCLVMVLSPCHVKEINIKFGPNSGSKVPLATVTVIDQSETKKKVFLWRTAAFWAFTVFLGDIILLTDVV
          Y.CLVMVLSPCHVKEINIKFGPNSG.KVPLATVTVIDQSET.KKVFL.RTAAFWA.TVFLGDIILL.DVV
Retrocopy YDCLVMVLSPCHVKEINIKFGPNSGPKVPLATVTVIDQSET-KKVFL*RTAAFWAYTVFLGDIILLADVV

Parental  IHEDQWIGETVLQSTFSSQLLNLGSYSSIQPEEYSSVVSDVVLQDLLAYVSSKHSYLRDLPPRQPQRVNS
          IHEDQW.GETVLQSTFSSQLLNLGSYSSIQPEEYSSVVSDVVLQDLLA.VSSKHSYLRDLPPRQPQRVNS
Retrocopy IHEDQWVGETVLQSTFSSQLLNLGSYSSIQPEEYSSVVSDVVLQDLLAHVSSKHSYLRDLPPRQPQRVNS

Parental  IDFVELEHLQPDVLVHAVLRVVDFTILTEAVYSYRGQKQKKVMLTVEQAQDQHYALVLWGPGAAWYPQLQ
          IDF.ELEHLQPDVLVH..LRVVDFTILTEAVYSYRGQKQKKVMLTVEQAQDQHY.LVLW.PGAAWYPQLQ
Retrocopy IDFIELEHLQPDVLVHTILRVVDFTILTEAVYSYRGQKQKKVMLTVEQAQDQHYVLVLWSPGAAWYPQLQ

Parental  RKKGVV
          RKKG..
Retrocopy RKKGYI

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	0.04 RPM	7.92 RPM
SRP007412_cerebellum	0.04 RPM	5.38 RPM
SRP007412_heart	0.00 RPM	6.67 RPM
SRP007412_kidney	0.00 RPM	24.84 RPM
SRP007412_liver	0.03 RPM	12.86 RPM
SRP007412_testis	0.00 RPM	4.64 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_941 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_941 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_941 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1370
Pongo abelii	retro_pabe_1137

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011809	1 retrocopy	retro_chof_1126,
Dasypus novemcinctus	ENSDNOG00000000017	1 retrocopy	retro_dnov_2237,
Homo sapiens	ENSG00000122376	1 retrocopy	retro_hsap_1370,
Nomascus leucogenys	ENSNLEG00000011652	3 retrocopies	retro_nleu_1073, retro_nleu_2157, retro_nleu_840,
Pongo abelii	ENSPPYG00000002828	1 retrocopy	retro_pabe_1137,
Pan troglodytes	ENSPTRG00000002465	1 retrocopy	retro_ptro_941 ,