RetrogeneDB ID: retro_ptro_3094

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:23580283..23580721(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C11H11ORF73
• Ensembl ID: ENSPTRG00000004144
• Aliases: C11H11orf73, C11orf73
• Description: Pan troglodytes lethal, Chr 7, Rinchik 6 (C11H11orf73), mRNA. [Source:RefSeq mRNA;Acc:NM_001242569]

Sequence

>retro_ptro_3094
GGCTCTGTCTACTTTTCCTATCCTGATTCAAATGGGATGCCAGTATGACAACTCCTATGATTTGTCATGAATGGGAAACC
AAGTGCCATCTTCAAAATTTCAGGTCTTAAATCTGGAGGAGGAAGCCAACATCCTTTTGGAGCCATGAATACTGTCCAAA
CTCCATCTGTTGCTCAGATTGGAATTTTGGTGAAATCACTGGACAGTATGGCTCAGCAGACTCCTGTAGGTAATGCTGCT
CTATCTTCAGTTGACTCATTCACTCTGTTCACACAAAAGATGTTGGACAACTTACACAATTTTGCTTCATCATTTGCTGT
CTCTCAGGCCCAGATGACACCAAGCCTATATGAAATGTTCATTCTGCAAAATATGTTTCTGAAATGGTACGAAAACTTTC
AAAGATGACTAGCACAGAACCCTGTCTTTTGGAAAACA

Alignment

ORF - retro_ptro_3094 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.62 %
• Parental protein coverage: 74.11 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSVYFSYPDSNGMPVWQLLGFVTNGKPSAIFKISGLKSGEGSQHPFGAMNIVRTPSVAQIGISVELLDSM
          GSVYFSYPDSNGMPV.QLL.FV.NGKPSAIFKISGLKSG.GSQHPFGAMN.V.TPSVAQIGI.V..LDSM
Retrocopy GSVYFSYPDSNGMPV*QLL*FVMNGKPSAIFKISGLKSGGGSQHPFGAMNTVQTPSVAQIGILVKSLDSM

Parental  AQQTPVGNAAVSSVDSFTQFTQKMLDNFYNFASSFAVSQAQMTPSPSEMFIPANVVLKWYENFQRRLAQN
          AQQTPVGNAA.SSVDSFT.FTQKMLDN..NFASSFAVSQAQMTPS..EMFI..N..LKWYENFQR.LAQN
Retrocopy AQQTPVGNAALSSVDSFTLFTQKMLDNLHNFASSFAVSQAQMTPSLYEMFILQNMFLKWYENFQR*LAQN

Parental  PLFWKT
          P.FWKT
Retrocopy PVFWKT

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	15.10 RPM
SRP007412_cerebellum	0.04 RPM	8.39 RPM
SRP007412_heart	0.00 RPM	13.99 RPM
SRP007412_kidney	0.00 RPM	11.61 RPM
SRP007412_liver	0.00 RPM	10.18 RPM
SRP007412_testis	0.00 RPM	6.64 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3094 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3094 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3094 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4658
Gorilla gorilla	retro_ggor_2891

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015605	1 retrocopy	retro_ecab_720,
Homo sapiens	ENSG00000149196	1 retrocopy	retro_hsap_4658,
Gorilla gorilla	ENSGGOG00000023168	1 retrocopy	retro_ggor_2891,
Myotis lucifugus	ENSMLUG00000016260	1 retrocopy	retro_mluc_784,
Mus musculus	ENSMUSG00000062797	1 retrocopy	retro_mmus_3722,
Nomascus leucogenys	ENSNLEG00000016224	1 retrocopy	retro_nleu_1095,
Oryctolagus cuniculus	ENSOCUG00000013108	2 retrocopies	retro_ocun_1147, retro_ocun_280,
Pongo abelii	ENSPPYG00000003746	1 retrocopy	retro_pabe_3618,
Pan troglodytes	ENSPTRG00000004144	1 retrocopy	retro_ptro_3094 ,
Tupaia belangeri	ENSTBEG00000009192	2 retrocopies	retro_tbel_1594, retro_tbel_3248,
Tursiops truncatus	ENSTTRG00000012267	1 retrocopy	retro_ttru_562,