RetrogeneDB ID: retro_ggor_2081

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 4:174443090..174443604(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YWHAQ
• Ensembl ID: ENSGGOG00000001569
• Aliases: None
• Description: None

Sequence

>retro_ggor_2081
AAGAAGTTGCAGCTGATTAAGGACTACCAGGAGAAAGTGGAGTCTGAGCTGAGATCGATCTGCACCACGGTCCTGGAATT
GTTGGATAAATATTTAACAGCCAATGCAACTAATCCAGAGAGTGGGGTCTTCTATCTGAAAATGAAGGGTGATTACTTCC
AGTACTTTGCTGAAGTTGCACGTGGTAATGATCAAAAACAAATGATAGATAATTCCCAAGGAGCTTAGCAAAAGGCATTT
GATATAAGCAAGAAAGAGATACAATCCACACATCCAATCTTCCTGGGGCTTGCTGTTAACTTTTCTGTATTTTACTATGA
GATTCTTAATAACCCAGAGCTTGCCTGCACGCTGGCTAAAATGGCTTTTGATGAGGCCATTGCAGAACTTGATACACTGA
ATGAAGATTCATCCAAAAGACAGCACCCTCATTATGGAGTTTCTTAGAGACAACCTAACACTATGGACCTCAGATAGTGC
AGGAGAAGAATGTGATGCAGCAGAAGGGGCTGAA

Alignment

ORF - retro_ggor_2081 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.37 %
• Parental protein coverage: 69.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKLQLIKDYREKVESELRSICTTVLELLDKYLIANATNPESKVFYLKMKGDYFRYLAEVACGDDRKQTID
          KKLQLIKDY.EKVESELRSICTTVLELLDKYL.ANATNPES.VFYLKMKGDYF.Y.AEVA.G.D.KQ.ID
Retrocopy KKLQLIKDYQEKVESELRSICTTVLELLDKYLTANATNPESGVFYLKMKGDYFQYFAEVARGNDQKQMID

Parental  NSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILNNPELACTLAKTAFDEAIAELDTLNEDSY-K
          NSQGA.Q.AFDISKKE.Q.THPI.LGLA.NFSVFYYEILNNPELACTLAK.AFDEAIAELDTLNEDS..K
Retrocopy NSQGA*QKAFDISKKEIQSTHPIFLGLAVNFSVFYYEILNNPELACTLAKMAFDEAIAELDTLNEDSS>K

Parental  DSTLIMQLLRDNLTLWTSDSAGEECDAAEGAE
          DSTLIM..LRDNLTLWTSDSAGEECDAAEGAE
Retrocopy DSTLIMEFLRDNLTLWTSDSAGEECDAAEGAE

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	0.10 RPM	122.23 RPM
SRP007412_cerebellum	0.00 RPM	111.50 RPM
SRP007412_heart	0.00 RPM	16.73 RPM
SRP007412_kidney	0.00 RPM	99.81 RPM
SRP007412_liver	0.00 RPM	42.81 RPM
SRP007412_testis	0.00 RPM	216.01 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2081 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2081 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3004
Pan troglodytes	retro_ptro_2032
Pongo abelii	retro_pabe_2490

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002108	2 retrocopies	retro_btau_1180, retro_btau_86,
Callithrix jacchus	ENSCJAG00000006394	2 retrocopies	retro_cjac_2197, retro_cjac_3127,
Echinops telfairi	ENSETEG00000015359	4 retrocopies	retro_etel_1027, retro_etel_1048, retro_etel_235, retro_etel_65,
Homo sapiens	ENSG00000134308	2 retrocopies	retro_hsap_3004, retro_hsap_8,
Gorilla gorilla	ENSGGOG00000001569	1 retrocopy	retro_ggor_2081 ,
Gorilla gorilla	ENSGGOG00000004580	2 retrocopies	retro_ggor_2795, retro_ggor_699,
Gorilla gorilla	ENSGGOG00000016840	1 retrocopy	retro_ggor_2596,
Gorilla gorilla	ENSGGOG00000022133	9 retrocopies	retro_ggor_1092, retro_ggor_1754, retro_ggor_211, retro_ggor_2379, retro_ggor_2997, retro_ggor_2998, retro_ggor_3020, retro_ggor_499, retro_ggor_544,
Myotis lucifugus	ENSMLUG00000005383	1 retrocopy	retro_mluc_1817,
Monodelphis domestica	ENSMODG00000014740	1 retrocopy	retro_mdom_1339,
Mustela putorius furo	ENSMPUG00000013252	2 retrocopies	retro_mputfur_1132, retro_mputfur_730,
Oryctolagus cuniculus	ENSOCUG00000010482	1 retrocopy	retro_ocun_1463,
Pongo abelii	ENSPPYG00000012663	4 retrocopies	retro_pabe_1165, retro_pabe_2490, retro_pabe_3391, retro_pabe_3511,
Pan troglodytes	ENSPTRG00000011641	2 retrocopies	retro_ptro_2032, retro_ptro_3,
Pteropus vampyrus	ENSPVAG00000005334	1 retrocopy	retro_pvam_983,
Rattus norvegicus	ENSRNOG00000008104	5 retrocopies	retro_rnor_1569, retro_rnor_2065, retro_rnor_2123, retro_rnor_2180, retro_rnor_2746,
Sorex araneus	ENSSARG00000012476	4 retrocopies	retro_sara_1, retro_sara_162, retro_sara_179, retro_sara_23,