RetrogeneDB ID: retro_ggor_2114

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 4:120373890..120374575(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LYPLA2
• Ensembl ID: ENSGGOG00000004330
• Aliases: None
• Description: None

Sequence

>retro_ggor_2114
ATGTGCAGCAATAACATGTCAGCCCCGCTGCCAGCCATCGTGCCTGCCGCCTGGAAGGCCACCGCGGAGGTGATTTTCCT
TCATGGATTGGGAGATACTGGGCACCGATGGATAGAAGCCTTTGCAGGTATCAGAAGTTCACATATCAAATATATCTGCC
TGCATGCTCCTGTTATGCCTTTACATTAAATATGAACATGGCTGTGCCTTCATGGTTTGATATTATTGGGCTTTCACCAG
ATTCACAGGAGGACGAACCTGGGATTAAACAGGCAGCAGAAAATATAAAAGCTTTGATCGATCAAGAAGTGAAGAATGGC
ATTCCTTCTAACCGAATTATTGTAGGAGGATTTTCTCAGGGAGGAGCTTTATCTTTATATACTGCCCTTACCACGTAGCA
GAAACTGGCGGGTGTCACTGCGCTCAGTTGCTGGCTTCCACTTCGGGCTTTATTTCCACAGGGTCCTATCAGGGGCGCTA
ACAGAGATATTTCTATTCTCCAGTGCCACGGAGATTGTGACCCGTTAGTTCCCCTGATGTTTGGTTCTCTTACGGTTGAA
AAACTAAAAACTTTGGCGATCCAGCCAATGTGACCTTTAAAACCTATGAAGGTATGATGCATAGCTCATGTCAACAGGAA
ATGATGGATGTCAAGCAATTCATTGATAAACTCCTACCTCCAATT

Alignment

ORF - retro_ggor_2114 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.68 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MCGNTMSVPLLTDAATVSGAERETAAVIFLHGLGDTGHSWADALSTIRLPHVKYICPHAPRIPV-TLNMK
          MC.N.MS.PL....A.V..A...TA.VIFLHGLGDTGH.W..A...IR..H.KYIC.HAP..P..TLNM.
Retrocopy MCSNNMSAPL---PAIVPAAWKATAEVIFLHGLGDTGHRWIEAFAGIRSSHIKYICLHAPVMPL<TLNMN

Parental  MVMPSWFDLMGLSPDAPEDEAGIKKAAENIKALIEHEMKNGIPANRIVLGGFSQGGALSLYTALTCPHPL
          M..PSWFD..GLSPD..EDE.GIK.AAENIKALI..E.KNGIP.NRI..GGFSQGGALSLYTALT....L
Retrocopy MAVPSWFDIIGLSPDSQEDEPGIKQAAENIKALIDQEVKNGIPSNRIIVGGFSQGGALSLYTALTT*QKL

Parental  AGIVALSCWLPLHRAFPQA-ANGSAKDLAILQCHGELDPMVPVRFGALTAEKLRSVV-TPARVQFKTYPG
          AG..ALSCWLPL...FPQ....G...D..ILQCHG..DP.VP..FG.LT.EKL......PA.V.FKTY.G
Retrocopy AGVTALSCWLPLRALFPQGPIRGANRDISILQCHGDCDPLVPLMFGSLTVEKLKTLA<DPANVTFKTYEG

Parental  VMHSSCPQEMAAVKEFLEKLLPPV
          .MHSSC.QEM..VK.F..KLLPP.
Retrocopy MMHSSCQQEMMDVKQFIDKLLPPI

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	14.58 RPM
SRP007412_cerebellum	0.00 RPM	18.75 RPM
SRP007412_heart	0.00 RPM	10.88 RPM
SRP007412_kidney	0.00 RPM	31.24 RPM
SRP007412_liver	0.00 RPM	19.86 RPM
SRP007412_testis	0.00 RPM	9.53 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_2114 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2114 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3078
Pongo abelii	retro_pabe_2550

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011625	1 retrocopy	retro_btau_1605,
Callithrix jacchus	ENSCJAG00000020914	1 retrocopy	retro_cjac_2585,
Dasypus novemcinctus	ENSDNOG00000011285	2 retrocopies	retro_dnov_1186, retro_dnov_134,
Gorilla gorilla	ENSGGOG00000004330	3 retrocopies	retro_ggor_2114 , retro_ggor_2413, retro_ggor_2626,
Macropus eugenii	ENSMEUG00000004768	2 retrocopies	retro_meug_1134, retro_meug_1526,
Microcebus murinus	ENSMICG00000005841	1 retrocopy	retro_mmur_1166,
Otolemur garnettii	ENSOGAG00000032260	1 retrocopy	retro_ogar_2866,
Pongo abelii	ENSPPYG00000001733	1 retrocopy	retro_pabe_142,
Tursiops truncatus	ENSTTRG00000016127	1 retrocopy	retro_ttru_1522,