RetrogeneDB ID: retro_ggor_1533

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 20:25796377..25797349(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIPAL1
• Ensembl ID: ENSGGOG00000009006
• Aliases: None
• Description: None

Sequence

>retro_ggor_1533
GGCTCCAGCTTCATATTGAAAAAGAACGGTCTCTTGCAACTGGCCAACAAAAGCGTCACTAGAGCTGGACAAGGTGGACA
TTCTGACCTGAAGGATGGCTCTGGGGGGCAGGAGTGCTGGCCATGGGAGCAGGAGAGGCTGCACATTTTGCTGCTTATGC
TTTTGCACCTGCCATCTTGGTCACCCTCACCCCCCCGGCCCTCTGAGTGTTCTCATAAGTGCAATATTATCTTCCTATTT
TTTAAATGAGCACTTGAACATTTATGGGAAAACAGACTGCATATTGGGGTCAACTGTGATGGTTATCCATGCCCCAGAAG
AAGAGGAAGTCACTTCTTTGCATGAAATGGAAATGAAATTGAGAGACCCAGGATTTATTTCCTTTGCTGTGATCATAATT
GTGATCTTGGTGCTGATTTTGATTGTGGCTCCCAAGAAAGGACAGACCAATATATTGGTCTATATTTCAATCTGTTCTTT
GGCTGCAGCATTTTCAATTTCTCCTGCCAAAGGCCTGGGTATTGCCATTAAGGAATTACTAGAATGGAAGCCAGTTTAGA
AGCATCCCCTGGTCATTGTTTTGCTGGCTATACTTGTGTTTTTGGTGACTACACAGATTAACTATCTCAAGGCACCAGAC
ACTGTTAATACATCTCCTGTGACTCCTATTTATTTTGCATTCTTCACATCCATGGTAGTGACTTGCTCTGCCATCTTACT
CCAAGAGTGGTATGGCATGAAAGCTGGAGATATCATCGAGACCCTGAATGGATTCTTCACTATTATCCTTGGCATCTTTC
TTCTACATGCTTTTAAAAATACTGACATTACCTGGAGTAAGCTGACATCCACTGCTAAGAAAGAAGTCATCTCTCTGAAT
GGCAGTGAGAGCAGTCCTGTTTTACTAGAGAACTTGGCGTGTTCAGCCCTGGATACAATGATAACGTTACCTTGTTTAGC
AGAACTGATGAT

Alignment

ORF - retro_ggor_1533 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.58 %
• Parental protein coverage: 80. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GSSFILKKKGLLQLASKGFTRAGQGGHSYLKE-WLWWVGLLSMGAGEAANFA--AYAFAPATLVTPL-GA
          GSSFILKK.GLLQLA.K..TRAGQGGHS.LK..WLW..G.L.MGAGEAA.FA..A.A.A.....TP..G.
Retrocopy GSSFILKKNGLLQLANKSVTRAGQGGHSDLKD<WLWGAGVLAMGAGEAAHFAAYAFAPAILVTLTPP<GP

Parental  LSVLISAILSSYFLNEHLNIHGKIGCILSILGSTVMVIHAPQEEEVTSLHEMEMKLRDPGFISFAVIITV
          LSVLISAILSSYFLNEHLNI.GK..C...ILGSTVMVIHAP.EEEVTSLHEMEMKLRDPGFISFAVII.V
Retrocopy LSVLISAILSSYFLNEHLNIYGKTDC---ILGSTVMVIHAPEEEEVTSLHEMEMKLRDPGFISFAVIIIV

Parental  ISLVLILIVAPKKGQTNILVYISICSLIGAFSVSSVKGLGIAIKELIEWKPVYKHPLVFVLLAVLVLSVT
          I.LVLILIVAPKKGQTNILVYISICSL..AFS.S..KGLGIAIKEL.EWKPV.KHPLV.VLLA.LV..VT
Retrocopy I-LVLILIVAPKKGQTNILVYISICSLAAAFSISPAKGLGIAIKELLEWKPV*KHPLVIVLLAILVFLVT

Parental  TQINYLNKALDTFNTSLVTPIYYVFFTSMVVTCSAILFQEWYGMTAGDIIGTLSGFLTIIIGIFLLHAFK
          TQINYL.KA.DT.NTS.VTPIY..FFTSMVVTCSAIL.QEWYGM.AGDII.TL.GF.TII.GIFLLHAFK
Retrocopy TQINYL-KAPDTVNTSPVTPIYFAFFTSMVVTCSAILLQEWYGMKAGDIIETLNGFFTIILGIFLLHAFK

Parental  NTDITWSELTSTAKKEAVSLNVNENNYVLLENLECSA-PGYNDDITLFSRTDD
          NTDITWS.LTSTAKKE..SLN..E...VLLENL.CSA.PGYND..TLFSRTDD
Retrocopy NTDITWSKLTSTAKKEVISLNGSESSPVLLENLACSA<PGYNDNVTLFSRTDD

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	0.24 RPM
SRP007412_cerebellum	0.00 RPM	0.32 RPM
SRP007412_heart	0.00 RPM	0.03 RPM
SRP007412_kidney	0.00 RPM	0.94 RPM
SRP007412_liver	0.03 RPM	1.50 RPM
SRP007412_testis	0.10 RPM	0.21 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_1533 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1533 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2463
Pan troglodytes	retro_ptro_1422

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002047	1 retrocopy	retro_dnov_2048,
Homo sapiens	ENSG00000163293	1 retrocopy	retro_hsap_2463,
Gorilla gorilla	ENSGGOG00000009006	1 retrocopy	retro_ggor_1533 ,
Macaca mulatta	ENSMMUG00000018625	1 retrocopy	retro_mmul_638,
Nomascus leucogenys	ENSNLEG00000017377	1 retrocopy	retro_nleu_2814,
Pongo abelii	ENSPPYG00000014714	1 retrocopy	retro_pabe_1810,
Pan troglodytes	ENSPTRG00000016038	1 retrocopy	retro_ptro_1422,