RetrogeneDB ID: retro_ggor_1658

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2a:110833185..110833611(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR2D
• Ensembl ID: ENSGGOG00000004723
• Aliases: None
• Description: None

Sequence

>retro_ggor_1658
ATGGCAGCAGGCGGCAGCGATCCACGGGCTGACGATGTAGAGGAGGACACTTCACAGCTCCTTTTTCCTAAAGAGTTTGA
AACAGCGGAGACCCTTCTAAATTCAGAAGTTCATATGCTTCTGGAACATCGAAAGCAATAGAACGAGAGTGCAGAGGATG
AACAGGAACTCTCAGAAGTCTTCATGAAAACAATGAAACTACAAAGGCCGTTTCAGTGGTTTCGAAAACAGAGAGACCAT
TGCCAGTGTTCGTAGCTTGTTACTCTAGAAAAACCTTCATAAATTTGAGTTGGTCTGTTTGGCCAACCTTTGCCCAGAGA
CTGCTGAGGAGTCCAAGGCTCTAATCCCAAACTTGGAGGGGTGGTTTGAAGTGAGGAGCTGCAGCAGGTTCTTGATGATA
TCCAGACAAAGCACAGCTTTCAGTAT

Alignment

ORF - retro_ggor_1658 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.62 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAGGSDPRAGDVEEDASQLIFPKEIEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTL-NY
          MAAGGSDPRA.DVEED.SQL.FPKE..FETAETLLNSEVHMLLEHRKQ.NESAEDEQELSEVFMKT..NY
Retrocopy MAAGGSDPRADDVEEDTSQLLFPKE--FETAETLLNSEVHMLLEHRKQ*NESAEDEQELSEVFMKTM>NY

Parental  TARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFE-DEELQQILDDIQT
          ..RFS.F.NRETIASVRSLLL.K.LHKFEL.CLANLCPETAEESKALIP.LEG.FE..EELQQ.LDDIQT
Retrocopy KGRFSGFENRETIASVRSLLL*KNLHKFELVCLANLCPETAEESKALIPNLEGWFE<SEELQQVLDDIQT

Parental  KRSFQY
          K.SFQY
Retrocopy KHSFQY

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	24.46 RPM
SRP007412_cerebellum	0.00 RPM	15.92 RPM
SRP007412_heart	0.00 RPM	11.13 RPM
SRP007412_kidney	0.00 RPM	23.63 RPM
SRP007412_liver	0.00 RPM	17.73 RPM
SRP007412_testis	0.10 RPM	103.50 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_1658 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1658 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1571
Pongo abelii	retro_pabe_1933
Macaca mulatta	retro_mmul_1011

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011746	1 retrocopy	retro_amel_1020,
Canis familiaris	ENSCAFG00000004311	2 retrocopies	retro_cfam_1403, retro_cfam_2188,
Choloepus hoffmanni	ENSCHOG00000013850	3 retrocopies	retro_chof_1003, retro_chof_1568, retro_chof_1920,
Dasypus novemcinctus	ENSDNOG00000008527	1 retrocopy	retro_dnov_734,
Felis catus	ENSFCAG00000027816	1 retrocopy	retro_fcat_1148,
Gorilla gorilla	ENSGGOG00000004723	1 retrocopy	retro_ggor_1658 ,
Macaca mulatta	ENSMMUG00000001989	1 retrocopy	retro_mmul_1011,
Monodelphis domestica	ENSMODG00000018653	4 retrocopies	retro_mdom_1320, retro_mdom_457, retro_mdom_689, retro_mdom_851,
Mustela putorius furo	ENSMPUG00000016685	1 retrocopy	retro_mputfur_611,
Mus musculus	ENSMUSG00000024258	1 retrocopy	retro_mmus_1331,
Oryctolagus cuniculus	ENSOCUG00000021449	1 retrocopy	retro_ocun_35,
Ochotona princeps	ENSOPRG00000005327	2 retrocopies	retro_opri_233, retro_opri_725,
Pongo abelii	ENSPPYG00000012759	1 retrocopy	retro_pabe_1933,
Pan troglodytes	ENSPTRG00000012436	1 retrocopy	retro_ptro_1571,
Sorex araneus	ENSSARG00000009037	1 retrocopy	retro_sara_420,
Sarcophilus harrisii	ENSSHAG00000014817	1 retrocopy	retro_shar_728,
Ictidomys tridecemlineatus	ENSSTOG00000023329	3 retrocopies	retro_itri_1323, retro_itri_145, retro_itri_600,