RetrogeneDB ID: retro_ggor_1075

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 14:333844..334510(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000027564
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TOMM40L
• Ensembl ID: ENSGGOG00000005720
• Aliases: None
• Description: None

Sequence

>retro_ggor_1075
CTGCCCAACCCGGGCACATTCCAGGAGTGCCACCGGAAGTGTAAGGAGCTGTTTCCCATTCAGATGGAGGGTGTCAAGCT
CACAGTCAACAAAGGGTTGAGTAACCGTTTCCAGGTGAACCACACAGTAGCCCTCAGCGCAATCAGGGAGTCCAACTACC
ACTTCGGGGTCACGTATGTGGGGACAAAGCAGCTGAGTCCCACAGAGGCGTTCCCTGTACTGGTAGGTGACATGGACAAC
AGCGGCAGTCTCAACGCTCAGGTCATTCACCAGCTGGGCCCCGGTCTCAGGTCCAAGATGGCCATCCAGACCCAGCAGTC
GAAGTTTGTGAACTGGCAGGTGGACGGGGAGTATCGGGGCTCTGACTCACAGCAGCCGTCACCCTGGGGAACCCAGACGT
CCTCGTGGGTTCAAGAATTCTCGAAGCCCACTACCTCCAGAGCATCAGGCCTTGCCTGGCCCTGGGCGGAGAGCTGGTCT
ACAACCGGCGGCCTGGGGACGAGGGCACTGTCATGTCTCTAGCTGGGAAATACACATTGAACAATTAACTGGTTGGCAAC
GGTAACGTTGAGCCAGGCGGGCATGCACGCAACATACTACCACAAAGCCAGTGACCAGTTGCAGGTGGGTGTGGATTTTG
AGGCCAGCACAAGGATGCAGGATACC

Alignment

ORF - retro_ggor_1075 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.82 %
• Parental protein coverage: 71.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LPNPGSFDELHRLCKDVFPAQMEGVKLVVNKVLSSHFQVAHTIHMSALGLPGYHLHAAYAGDWQLSPTEV
          LPNPG.F.E.HR.CK..FP.QMEGVKL.VNK.LS..FQV.HT...SA.....YH....Y.G..QLSPTE.
Retrocopy LPNPGTFQECHRKCKELFPIQMEGVKLTVNKGLSNRFQVNHTVALSAIRESNYHFGVTYVGTKQLSPTEA

Parental  FPTVVGDMDSSGSLNAQVLLLLAERLRAKAVFQTQQAKFLTWQFDGEYRGDD-YTATLTLGNPDLIGESV
          FP..VGDMD.SGSLNAQV...L...LR.K...QTQQ.KF..WQ.DGEYRG.D..TA..TLGNPD....S.
Retrocopy FPVLVGDMDNSGSLNAQVIHQLGPGLRSKMAIQTQQSKFVNWQVDGEYRGSD<LTAAVTLGNPDVLVGSR

Parental  IMVAHFLQSLTHRLVLGGELVYHRRPGEEGAILTLAGKYSAVH-WVATLNVGSG-GAHASYYHRANEQVQ
          I..AH.LQS....L.LGGELVY.RRPG.EG....LAGKY......V...NV..G.G.HA.YYH.A..Q.Q
Retrocopy ILEAHYLQSIRPCLALGGELVYNRRPGDEGTVMSLAGKYTLNN*LVGNGNVEPG>GMHATYYHKASDQLQ

Parental  VGVEFEANTRLQDT
          VGV.FEA.TR.QDT
Retrocopy VGVDFEASTRMQDT

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	0.19 RPM	26.85 RPM
SRP007412_cerebellum	0.08 RPM	15.84 RPM
SRP007412_heart	0.06 RPM	11.04 RPM
SRP007412_kidney	0.00 RPM	17.83 RPM
SRP007412_liver	0.11 RPM	20.39 RPM
SRP007412_testis	2.38 RPM	4.14 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_1075 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1075 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000004808	1 retrocopy	retro_eeur_472,
Echinops telfairi	ENSETEG00000015755	2 retrocopies	retro_etel_1124, retro_etel_1461,
Gorilla gorilla	ENSGGOG00000005720	2 retrocopies	retro_ggor_1075 , retro_ggor_1761,
Gorilla gorilla	ENSGGOG00000023033	1 retrocopy	retro_ggor_1356,
Otolemur garnettii	ENSOGAG00000013733	1 retrocopy	retro_ogar_2524,
Ictidomys tridecemlineatus	ENSSTOG00000003800	2 retrocopies	retro_itri_301, retro_itri_724,
Drosophila melanogaster	FBgn0016041	1 retrocopy	retro_dmel_74,