RetrogeneDB ID: retro_ggor_1356

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 17:60203859..60204450(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000023561
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TOMM40
• Ensembl ID: ENSGGOG00000023033
• Aliases: None
• Description: None

Sequence

>retro_ggor_1356
GGGGGTGCCGAGGATGGGGCCTGCCGCTACCTGCCCAACCCCTGCACATTCGAGGAGTGCCACCGGAAGTGCAAGGAGCT
GTAGATGGAAGGTGTCAAGTTCACAGTGAACAAAGCGTTGTGTAAGCATTTTCAGGGGAACCACACAGTAACCCTCAGCA
CAATCAGGGAGTCCAACCACCATTTTGGTGTCAAGTATATGGGGACAAAGCAGCTGAGTCCCACAGAGGCATTCCCTGTA
CTGGTGGGTGACATGGACAACAGTGGCAGCCTCAATGCTCAGGTCATTCACCAGCTGGGCCCCGGCCTCAGGTCCAAGAT
GGCCATCCAGACCCAGCAGTCAAAGTTTGGGAAGTGGCAGGTGGATGGGGAGTACCAGGGCTCTGACTTCACAGTGGACG
TCACTCTGGGGAACCCAGACGTCTTGATGGGTTCAGGAATCCTCGTAGCCCACTACCTCCAGAGCATCATGCCTTGCCTG
GCACTGGGCAGTGAGCTGGTCTACCACCGACGGCCTGGGGATGAGGGCACTGTCATGTCTGTAGCTGGGAAATACACATT
GAACAACTGGTTGGCAACGGTAACGTTGGGT

Alignment

ORF - retro_ggor_1356 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74. %
• Parental protein coverage: 67.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GAAEDGACGCLPNPGTFEECHRKCKELFPIQMEGVKLTVNKGLSNHFQVNHTVALSTIGESNYHFGVTYV
          G.AEDGAC..LPNP.TFEECHRKCKE.....MEGVK.TVNK.L..HFQ.NHTV.LSTI.ESN.HFGV.Y.
Retrocopy GGAEDGACRYLPNPCTFEECHRKCKE---L*MEGVKFTVNKALCKHFQGNHTVTLSTIRESNHHFGVKYM

Parental  GTKQLSPTEAFPVLVGDMDNSGSLNAQVIHQLGPGLRSKMAIQWRDTGTQTWTSVQQVPATALTSAV--G
          GTKQLSPTEAFPVLVGDMDNSGSLNAQVIHQLGPGLRSKMAIQ........W...........T..V..G
Retrocopy GTKQLSPTEAFPVLVGDMDNSGSLNAQVIHQLGPGLRSKMAIQTQQSKFGKWQVDGEYQGSDFTVDVTLG

Parental  NP---WSMGILVAHYLQSITPCLALGGELVYHRRPGEEGTVMSLAGKYTLNNWLATVTLG
          NP......GILVAHYLQSI.PCLALG.ELVYHRRPG.EGTVMS.AGKYTLNNWLATVTLG
Retrocopy NPDVLMGSGILVAHYLQSIMPCLALGSELVYHRRPGDEGTVMSVAGKYTLNNWLATVTLG

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	22.68 RPM
SRP007412_cerebellum	0.00 RPM	16.27 RPM
SRP007412_heart	0.00 RPM	11.76 RPM
SRP007412_kidney	0.00 RPM	13.13 RPM
SRP007412_liver	0.00 RPM	8.41 RPM
SRP007412_testis	0.21 RPM	10.67 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_1356 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1356 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3159

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000005720	2 retrocopies	retro_ggor_1075, retro_ggor_1761,
Gorilla gorilla	ENSGGOG00000023033	1 retrocopy	retro_ggor_1356 ,
Microcebus murinus	ENSMICG00000014041	1 retrocopy	retro_mmur_420,
Myotis lucifugus	ENSMLUG00000028928	1 retrocopy	retro_mluc_697,
Nomascus leucogenys	ENSNLEG00000001726	2 retrocopies	retro_nleu_2368, retro_nleu_2542,
Oryctolagus cuniculus	ENSOCUG00000023582	1 retrocopy	retro_ocun_1143,
Pongo abelii	ENSPPYG00000025858	1 retrocopy	retro_pabe_174,
Pan troglodytes	ENSPTRG00000011126	1 retrocopy	retro_ptro_39,
Ictidomys tridecemlineatus	ENSSTOG00000009019	1 retrocopy	retro_itri_150,
Drosophila melanogaster	FBgn0016041	1 retrocopy	retro_dmel_74,