RetrogeneDB ID: retro_ggor_2040

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 4:77674136..77675310(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPOPL
• Ensembl ID: ENSGGOG00000016285
• Aliases: None
• Description: None

Sequence

>retro_ggor_2040
ATGTCTCAGGAACCTGCCCCACCTCTACCTAGAGATAAGTCTTCTTGTCCCATAGTAGAAAGCTAGTGTTATACACAGAT
CAAAATAGTAAAATGTTCAACACATAGACAATTAATAACTTCAGTTTTTGTCAAGAGGAAATGGGTGAGGCGTTAAAAAG
TTCCAAATTTTCACCTGGCCCAAATGACAAAATGAAATGGTGCCTGAGGGTAAACCCAAAAGCATTAGATAATGAAAGTA
AAGACTACTTGGTCCTCATATTTGCTTTTAGTCAGATGCCCCAAAAGTGAAGTGTGAGCAAAATTCAAATGTTCCCTTCT
GAATGCTAAAAGGGAAGAAACAAAAGCAATGGAAAGCCAAAGAGCGTATCAATTTGTGCAAGGGAAGGGCTGGGATTTTT
AAAAATTCATTAGAAGAGACCTTTTGCTTGACGAAGCTAATAGTCTTTGACCAGATGACAAGCTTACATTATTTTACGAG
ATGAGTGTGATCCAAGATTCAGTAAACAAATCAGGACATACTAATGCAAATACTTTCAAGATGCCTGAGGGTCGACTAGG
AGAAGACTGAGGTAATCTCTGGGAAAACACAAGATTTATAGACTGCAGTTTTTAGTGAGAGGACAAGAATTTAAAGCTCA
TAAATCTGCTTGTACCTGAATCCCTAGTTTTTAATGCCATGTTTGAACATGAAATGGAAGAAAGCATAAAGAATTGAGTG
GAAATAAATGATTTAGACCCTGATGTTTTTAAAGAAATGGTGAGATTCCTTAACACAGTGAAAGGATTAAACCTTGACAA
AATGGCTGACAACTTGTTGGCAGGTGCAGACAAACATGCACTGGGAACAGCTGAAGGTCTTGTGTGAGGAAGCTTTGTGT
AGTAATCCCTCAGTAGAAAATGTTGCTGATACCCTTGTCCTTGCAGATTTGCATGTTGCAAAACAGTTGAAAACAAAAGC
CATAGACATTATTAATAGGTGCAGTGTACTTCAACAACTTGGGTGTAAAGATTAGAAAAACTGAAACAGCAACCAAGCAA
CCAATGTAATGGAAACATCAGGGTGGAAGTCCATGATTCAGTCTCACCCTTACTTAGCAGCAGAAGCCTCCTGAGCACTA
GCATCTGCACAGTGTCCACAGTTTGGTATTCCACACACACGGCTAAAACAGTCC

Alignment

ORF - retro_ggor_2040 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.95 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 12
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSREPTPPLPGDMSTGPIAESWCYTQVKVV-KFSYMWTINNFSFCREEMGEVLKSSTFSSGPSDKMKWCL
          MS.EP.PPLP.D.S..PI.ES.CYTQ.K.V.K.....TINNFSFC.EEMGE.LKSS.FS.GP.DKMKWCL
Retrocopy MSQEPAPPLPRDKSSCPIVES*CYTQIKIV<KMFNT*TINNFSFCQEEMGEALKSSKFSPGPNDKMKWCL

Parental  RVNPKGLDDESKDYLSL-YLLLVSCPKSEVRAKFKFSLLNAKREETKAMESQRAYRFVQGKDWGFKKFIR
          RVNPK.LD.ESKDYL.L.YLLLV.CPKSEV.AKFK.SLLNAKREETKAMESQRAY.FVQGK.W.F.KFIR
Retrocopy RVNPKALDNESKDYLVL>YLLLVRCPKSEV*AKFKCSLLNAKREETKAMESQRAYQFVQGKGWDF*KFIR

Parental  RDFLLDEANGLLPDDKLTLFCEVSVVQDSVNISGHTNTNTLKVPECRLAEDLGNLWENTRFTDCSFFVRG
          RD.LLDEAN.L.PDDKLTLF.E.SV.QDSVN.SGHTN.NT.K.PE.RL.ED.GNLWENTRF.DCSF....
Retrocopy RDLLLDEANSL*PDDKLTLFYEMSVIQDSVNKSGHTNANTFKMPEGRLGED*GNLWENTRFIDCSF**ED

Parental  QEFKAHKSVLAARSPVFNAMFEHEMEESKKNRVEINDLDPEVFKEMMRFIYTGRAPNLDKMADNLLAAAD
          ...K.....L...S.VFNAMFEHEMEES.KN.VEINDLDP.VFKEM.RF..T....NLDKMADNLLA.AD
Retrocopy KNLKLI-NLLVPESLVFNAMFEHEMEESIKN*VEINDLDPDVFKEMVRFLNTVKGLNLDKMADNLLAGAD

Parental  KYAL-ERLKVMCEEALCSNLSVENVADTLVLADLHSAEQLKAQAIDFINRCSVLRQLGCKDGKNWNGNQA
          K.AL.E.LKV.CEEALCSN.SVENVADTLVLADLH.A.QLK..AID.INRCSVL.QLGCKD.KN.N.NQA
Retrocopy KHAL>EQLKVLCEEALCSNPSVENVADTLVLADLHVAKQLKTKAIDIINRCSVLQQLGCKD*KN*NSNQA

Parental  TDIMETSGWKSMIQSHPHLVAEAFRALASAQCPQFGIPRKRLKQS
          T..METSGWKSMIQSHP.L.AEA..ALASAQCPQFGIP..RLKQS
Retrocopy TNVMETSGWKSMIQSHPYLAAEAS*ALASAQCPQFGIPHTRLKQS

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	13.95 RPM
SRP007412_cerebellum	0.00 RPM	15.88 RPM
SRP007412_heart	0.00 RPM	3.13 RPM
SRP007412_kidney	0.04 RPM	23.84 RPM
SRP007412_liver	0.00 RPM	16.35 RPM
SRP007412_testis	0.00 RPM	19.89 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_2040 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2040 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000014763	1 retrocopy	retro_dnov_546,
Homo sapiens	ENSG00000144228	2 retrocopies	retro_hsap_2943, retro_hsap_3048,
Gorilla gorilla	ENSGGOG00000016285	1 retrocopy	retro_ggor_2040 ,
Macaca mulatta	ENSMMUG00000002560	2 retrocopies	retro_mmul_1884, retro_mmul_1885,
Nomascus leucogenys	ENSNLEG00000013800	1 retrocopy	retro_nleu_1629,
Oryctolagus cuniculus	ENSOCUG00000006944	1 retrocopy	retro_ocun_1842,
Pongo abelii	ENSPPYG00000012825	4 retrocopies	retro_pabe_2438, retro_pabe_2439, retro_pabe_2440, retro_pabe_2599,
Pan troglodytes	ENSPTRG00000012504	2 retrocopies	retro_ptro_1991, retro_ptro_2054,