RetrogeneDB ID: retro_pabe_3618

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:23447900..23448266(+)
• Located in intron of: ENSPPYG00000020187

Retrocopy information

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

Parental gene information

• Parental gene symbol: C11orf73
• Ensembl ID: ENSPPYG00000003746
• Aliases: None
• Description: chromosome 11 open reading frame 73 [Source:HGNC Symbol;Acc:26938]

Sequence

>retro_pabe_3618
GGGAAACCAAGTGCCATCTTCAAAATTTCAGGTCTTAAATCTGGAGGAGGAAGCCAACATCCTTTTGGAGCCATGAATAT
TGTCCAAACTCCATCTGTTGCGCAGATAGGAATTTCGGTGGAATCATTGGACAGTATGGCTCAGCAGACTCCTGTAGGTA
ATGCCGCTGTATTCTCAGTTGACTCATTCACTCTGTTCACGCAAAAGATGTTGGACAACTTATACAACTTTGCTTCATCG
TTTGCTGTCTCTCAGGACCAGATGACACCAAGCCTATATGAAATGTTCATTCTACAAAATGTGTTTCTGAAATGGTATGA
AAACTTTCAAAGATGACTACCACAGAACCCTCTCTTTTGGAAAACA

Alignment

ORF - retro_pabe_3618 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.52 %
• Parental protein coverage: 61.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GKPSAIFKISGLKSGEGSQHPFGAMNIVRTPSVAQIGISVELLDSMAQQTPVGNAAVSSVDSFTQFTQKM
          GKPSAIFKISGLKSG.GSQHPFGAMNIV.TPSVAQIGISVE.LDSMAQQTPVGNAAV.SVDSFT.FTQKM
Retrocopy GKPSAIFKISGLKSGGGSQHPFGAMNIVQTPSVAQIGISVESLDSMAQQTPVGNAAVFSVDSFTLFTQKM

Parental  LDNFYNFASSFAVSQAQMTPSPSEMFIPANVVLKWYENFQRRLAQNPLFWKT
          LDN.YNFASSFAVSQ.QMTPS..EMFI..NV.LKWYENFQR.L.QNPLFWKT
Retrocopy LDNLYNFASSFAVSQDQMTPSLYEMFILQNVFLKWYENFQR*LPQNPLFWKT

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	0.06 RPM	10.01 RPM
SRP007412_cerebellum	2.68 RPM	15.56 RPM
SRP007412_heart	0.00 RPM	9.42 RPM
SRP007412_kidney	0.00 RPM	10.84 RPM
SRP007412_liver	0.00 RPM	12.06 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3618 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3618 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3618 has 0 orthologous retrocopies within eutheria group .

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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,