RetrogeneDB ID: retro_ggor_547

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 10:123309821..123310572(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PHB2
• Ensembl ID: ENSGGOG00000004281
• Aliases: None
• Description: None

Sequence

>retro_ggor_547
GCCATCTTCTTCAATTATATCGGTGGCATGCAGCAGGACACTATCCTGGCCAAAGGCTTCATTTCAGGATTCCCTGGTCT
CGGCACCCCATCAACGATGACATTCTGGCCGGACCTTGAAAAATTTCCTCCCTAACAGGCTCAAAAGACCGGCAGATGGT
GAACATATCCCTGTACATGGTGTCTCAACCCAATGTTCAGGAGCTTCCTAGCATGCACAAGCACCTAGGGCTAGACAACA
AAGAATGAGTGTTGCCATCCATTGTCAAAAGAGTACTCAAGAGTGTGGTGGCCAAGTTCAATGCCTCATAGCTGATTACC
CAGTGGGCTCGAGTATCCCTGTTGATTCAATGGGAGCTGCCAGAGAGGGCCAAGGACTTCAGTCTTATCTTGGATGATGT
AGCCATCACAGAGCTGAGCTTCAGCTGAGAGTACACAGCTATTGTAGAGGCCAAACAAGTGGTCCAGCAGGAGGCCCAGC
AGGCCCAGTTCTTGGTAGAAAAAGCAAAACTAGAACACCAGCAAAAGACTGCCCAGGCTAAGTGTGAAGCTGAGGCTGCT
AAGATGCTTGGGGAAGCACTGAGCAAGAACCCTGGCTACATCAAAATTCATAAGATTAGGCAGCCCAGAACATCTCCAAG
ACAATCACATCACAGAATCATATCTGTCTCACTGATGACAATCTTGTGCTGCACTTACAGGATAAGACTTTCACCTGGGG
AAATAAAGGCAGCCTCATTAAGGGTAAGAAA

Alignment

ORF - retro_ggor_547 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.77 %
• Parental protein coverage: 83.95 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AIFFNRIGGVQQDTILAEG-LHFRIPWFQYPIIYDIRARPRKISSPTGSKDLQMVNISLRVLSRPNAQEL
          AIFFN.IGG.QQDTILA.G.LHFRIPW...PI..DI.A.P.KISS.TGSKD.QMVNISL...S.PN.QEL
Retrocopy AIFFNYIGGMQQDTILAKG<LHFRIPWSRHPINDDILAGP*KISSLTGSKDRQMVNISLYMVSQPNVQEL

Parental  PSMYQRLGLDYEERVLPSIVNEVLKSVVAKFNASQLITQRAQVSLLIRRELTERAKDFSLILDDVAITEL
          PSM...LGLD..E.VLPSIV..VLKSVVAKFNAS.LITQ.A.VSLLI..EL.ERAKDFSLILDDVAITEL
Retrocopy PSMHKHLGLDNKE*VLPSIVKRVLKSVVAKFNAS*LITQWARVSLLIQWELPERAKDFSLILDDVAITEL

Parental  SFSREYTAAVEAKQVAQQEAQRAQFLVEKAKQEQRQKIVQAEGEAEAAKMLGEALSKNPGYIKLRKIR-A
          SFS.EYTA.VEAKQV.QQEAQ.AQFLVEKAK.E..QK..QA..EAEAAKMLGEALSKNPGYIK..KIR.A
Retrocopy SFS*EYTAIVEAKQVVQQEAQQAQFLVEKAKLEHQQKTAQAKCEAEAAKMLGEALSKNPGYIKIHKIR<A

Parental  AQNISKTIATSQNRIYLTADNLVLNLQDESFT-SYSDSLIKGKK
          AQNISKTI.TSQN.I.LT.DNLVL.LQD..FT.....SLIKGKK
Retrocopy AQNISKTI-TSQNHICLTDDNLVLHLQDKTFTWGNKGSLIKGKK

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	41.91 RPM
SRP007412_cerebellum	0.04 RPM	40.03 RPM
SRP007412_heart	0.00 RPM	46.59 RPM
SRP007412_kidney	0.00 RPM	77.24 RPM
SRP007412_liver	0.00 RPM	91.69 RPM
SRP007412_testis	0.00 RPM	35.85 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_547 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_547 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013760	1 retrocopy	retro_amel_1928,
Canis familiaris	ENSCAFG00000014439	1 retrocopy	retro_cfam_1885,
Callithrix jacchus	ENSCJAG00000007137	1 retrocopy	retro_cjac_781,
Homo sapiens	ENSG00000215021	1 retrocopy	retro_hsap_624,
Gorilla gorilla	ENSGGOG00000004281	1 retrocopy	retro_ggor_547 ,
Macaca mulatta	ENSMMUG00000010205	2 retrocopies	retro_mmul_2599, retro_mmul_2623,
Nomascus leucogenys	ENSNLEG00000005021	2 retrocopies	retro_nleu_121, retro_nleu_450,
Pongo abelii	ENSPPYG00000004214	3 retrocopies	retro_pabe_419, retro_pabe_557, retro_pabe_559,
Rattus norvegicus	ENSRNOG00000012999	1 retrocopy	retro_rnor_2373,