RetrogeneDB ID: retro_ggor_1761

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2b:18648498..18649302(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_ggor_1761
CTGCCCAACCCGGGCACATTCGGGGAGTGCCACCGGAAGTGCAAGGAGCTGTTTCCCATTCAGATGGAGGGTGTCAAGCT
CATAGTCAACAAAGGGTTGAGTAACCATTTCCAGGTGAACCACACAGTAGCCCTCAGCACAATCAGGGAGTCCAACTACC
ACTTCGGGGTCACGTATGTGGGGACAAAGCAGCTGAGTCCCATAGAGGCGTTCCTTGTATTGGTGGGTGACATGGACAAC
AGCGGCAGTCTCAACGCTCAGGTCATTCACCAGCTGGGCCCCGGTCTCAGGTCCAAGATGGCCATCCAGACCCAGCAGTC
GAAGTTTGTGAACTGGCAGGTGGACGGGGAGTATCGGGGCTCTGACTGACAGCAGCCGTCACCCTGGGGAAACCCAGACG
TCCTCGTGGGTTCAGGAATCCTCGTAGCCCACTACCTCCAGAGCATCACGCCTTGCCTGGCCCTGGGCGGAGAGCTGGTC
TACCACCAGCAGCCTGGGGAGGAGAGCACTGTCATGTCTCCAGCTGGGAAATACACATTGAACAACTGGTTGGCAACGGT
AACGTTGGGCCAGGCGGGCATGCACGCAACATACTACCACAAAGCCAGTGACCAGCTGCAGGTGGGTGTGGAGTTTGAGG
CCAACACAAGGATGCAGGACACCAGCATCTCCTTCGGGTACCAGCTGGACCTGCCCAAGGCCAAAGGCTCTGTGGATAGC
AACTGGATCGTGTGTGCCACGTTGGAGAAGAAGCTCCCGCCCCTGCCCCTGACACTGGCCCCTGGGGCCTTCCTGAATCA
CTTC

Alignment

ORF - retro_ggor_1761 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.93 %
• Parental protein coverage: 88.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPNPGSFDELHRLCKDVFPAQMEGVKLVVNKVLSSHFQVAHTIHMSALGLPGYHLHAAYAGDWQLSPTEV
          LPNPG.F.E.HR.CK..FP.QMEGVKL.VNK.LS.HFQV.HT...S......YH....Y.G..QLSP.E.
Retrocopy LPNPGTFGECHRKCKELFPIQMEGVKLIVNKGLSNHFQVNHTVALSTIRESNYHFGVTYVGTKQLSPIEA

Parental  FPTVVGDMDSSGSLNAQVLLLLAERLRAKAVFQTQQAKFLTWQFDGEYRGDDYTATLTLGNPDLIGESVI
          F...VGDMD.SGSLNAQV...L...LR.K...QTQQ.KF..WQ.DGEYRG.D.......GNPD....S.I
Retrocopy FLVLVGDMDNSGSLNAQVIHQLGPGLRSKMAIQTQQSKFVNWQVDGEYRGSD*QQPSPWGNPDVLVGSGI

Parental  MVAHFLQSLTHRLVLGGELVYHRRPGEEGAILTLAGKYSAVHWVATLNVGSGGAHASYYHRANEQVQVGV
          .VAH.LQS.T..L.LGGELVYH..PGEE......AGKY....W.AT...G..G.HA.YYH.A..Q.QVGV
Retrocopy LVAHYLQSITPCLALGGELVYHQQPGEESTVMSPAGKYTLNNWLATVTLGQAGMHATYYHKASDQLQVGV

Parental  EFEANTRLQDTTFSFGYHLTLPQANMVFRGLVDSNWCVGAVLEKKMPPLPVTLALGAFLNHW
          EFEANTR.QDT..SFGY.L.LP.A.....G.VDSNW.V.A.LEKK.PPLP.TLA.GAFLNH.
Retrocopy EFEANTRMQDTSISFGYQLDLPKA----KGSVDSNWIVCATLEKKLPPLPLTLAPGAFLNHF

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	1.20 RPM	26.85 RPM
SRP007412_cerebellum	1.26 RPM	15.84 RPM
SRP007412_heart	0.78 RPM	11.04 RPM
SRP007412_kidney	0.94 RPM	17.83 RPM
SRP007412_liver	0.79 RPM	20.39 RPM
SRP007412_testis	1.86 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_1761 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1761 has 0 orthologous retrocopies within eutheria group .

---

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,