RetrogeneDB ID: retro_ggor_2893

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:25333994..25334682(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000025838
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PAFAH1B2
• Ensembl ID: ENSGGOG00000028197
• Aliases: None
• Description: None

Sequence

>retro_ggor_2893
ATGAACCAAGGAGACTCAAACCCAGCAGCTATTCCGCATGCGGCAGAAGACATTCAAGGAGATGACAGATGGATGTGTCA
GCACAACAGATTTGTTTTGGACTGTAAAGACAAACAGCCTGATGTACCATTTGCGGGAGGCTCCGTGGTGCAGTTACTGC
AGCCATATGAGATATGGCGAGAGCTTTTTTCCCCACTTCATGCACTGAATTTTGGAACTGGGGGAGATACAACAAGCCAT
GTTTTGTGGAGACTAAAGAACGGAGAACTGGGGAATACTAAGCCTAAGGTCATTGTTTTCTGGCTAGGAAGAAACAACCA
TGAAAATATGGCAGAAGAGGTAGCAGGTGGTATGGCGGCCATCGTACAACTTATCAACACAAGGCAGCCACAGGCCAAAA
TCATTATATTTGATCTGTTACCTCAAGGTGAGAAACCCAACCCTTTGAGGCAAAAGAACGCCAAGGTGAACCCACTCGTC
AAGATTTCGCTGCTGAAACTTAACCAACGTGCAGCTCCTGCATACTGACAGGGGTTTCGTGCACTCCGACCGTGCCATCT
CCTGCCACGACATGTTTGATTTTCTGCATTTGACAGGAGGCGGCTACTCAAAGGTCTGCAAACCCTTGAATGAACTGATC
ATGCAGTTGTTGGAGGAAACACCTGAGGAGAAACAAACCACCATTGCC

Alignment

ORF - retro_ggor_2893 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.16 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSQGDSNPAAIPHAAEDIQGDDRWMSQHNRFVLDCKDKEPDVLFVGDSMVQLMQQYEIWRELFSPLHALN
          M.QGDSNPAAIPHAAEDIQGDDRWM.QHNRFVLDCKDK.PDV.F.G.S.VQL.Q.YEIWRELFSPLHALN
Retrocopy MNQGDSNPAAIPHAAEDIQGDDRWMCQHNRFVLDCKDKQPDVPFAGGSVVQLLQPYEIWRELFSPLHALN

Parental  FGIGGDTTRHVLWRLKNGELENIKPKVKLYLCIYTTNRERRKVSRGGCIKFEPGMVRRKRPQPGHVGFGL
          FG.GGDTT.HVLWRLKNGEL.N.KPKV.........N.E.......G.............PQ.....F.L
Retrocopy FGTGGDTTSHVLWRLKNGELGNTKPKV-IVFWLGRNNHENMAEEVAGGMAAIVQLINTRQPQAKIIIFDL

Parental  LPRGEKPNPLRQKNAKVNQLLKVSLPK-LANVQLLDTDGGFVHSDGAISCHDMFDFLHLTGGGYAKICKP
          LP.GEKPNPLRQKNAKVN.L.K.SL.K.L.NVQLL.TD.GFVHSD.AISCHDMFDFLHLTGGGY.K.CKP
Retrocopy LPQGEKPNPLRQKNAKVNPLVKISLLK>LTNVQLLHTDRGFVHSDRAISCHDMFDFLHLTGGGYSKVCKP

Parental  LHELIMQLLEETPEEKQTTIA
          L.ELIMQLLEETPEEKQTTIA
Retrocopy LNELIMQLLEETPEEKQTTIA

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	0.86 RPM	21.77 RPM
SRP007412_cerebellum	0.95 RPM	15.92 RPM
SRP007412_heart	0.34 RPM	3.44 RPM
SRP007412_kidney	0.82 RPM	10.51 RPM
SRP007412_liver	0.40 RPM	5.70 RPM
SRP007412_testis	1.14 RPM	22.79 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_2893 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2893 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4661
Pan troglodytes	retro_ptro_3097
Pongo abelii	retro_pabe_3621
Macaca mulatta	retro_mmul_2481

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008628	2 retrocopies	retro_amel_1145, retro_amel_818,
Canis familiaris	ENSCAFG00000013226	1 retrocopy	retro_cfam_1335,
Callithrix jacchus	ENSCJAG00000012698	1 retrocopy	retro_cjac_3325,
Dipodomys ordii	ENSDORG00000011274	1 retrocopy	retro_dord_560,
Felis catus	ENSFCAG00000029945	1 retrocopy	retro_fcat_270,
Homo sapiens	ENSG00000168092	2 retrocopies	retro_hsap_1148, retro_hsap_4661,
Gorilla gorilla	ENSGGOG00000028197	2 retrocopies	retro_ggor_2893 , retro_ggor_893,
Macaca mulatta	ENSMMUG00000002050	2 retrocopies	retro_mmul_2481, retro_mmul_892,
Mustela putorius furo	ENSMPUG00000004246	1 retrocopy	retro_mputfur_898,
Nomascus leucogenys	ENSNLEG00000007337	2 retrocopies	retro_nleu_1096, retro_nleu_946,
Pongo abelii	ENSPPYG00000003907	2 retrocopies	retro_pabe_3621, retro_pabe_953,
Pan troglodytes	ENSPTRG00000004318	2 retrocopies	retro_ptro_3097, retro_ptro_782,
Rattus norvegicus	ENSRNOG00000018032	1 retrocopy	retro_rnor_2585,
Sarcophilus harrisii	ENSSHAG00000011403	1 retrocopy	retro_shar_617,