RetrogeneDB ID: retro_hsap_624

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 10:111288018..111288769(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000232728
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PHB2
• Ensembl ID: ENSG00000215021
• Aliases: PHB2, BAP, BCAP37, Bap37, PNAS-141, REA, p22
• Description: prohibitin 2 [Source:HGNC Symbol;Acc:30306]

Sequence

>retro_hsap_624
GCCATCTTCTTCAATTATATCGGTGGCATGCAGCAAGACACTATCCTGGCCAAAGGCTTCATTTCAGGATTCCCTGGTCT
CGGTACCCCATCAACGATGACATTCTGGCCGGACCTTGAAAAATTTCCTCCCTAACAGGCTCAAAAGACCTGCAGATGGT
GAACATATCCCTGTACATGGTGTCTCAACCCAATGTTCAGGAGCTTCCTAGCATGCACAAGCACCTAGGGCTAGACAACA
AAGAATGAGTGTTGCCATCCATTGTCAAAAGAGTACTCAAGAGTGTGGTGGCCAAGTTCAATGCCTCATAGCTGATTACC
CAGTGGGCCCAGGTATCCCTGTTGATTCATTGGGAGCTGCCAGAGAGGGCCAAGGACTTCAGTCTTATCTTGGATGATGT
AGCCATCACAGAGCTGAGCTTTAGCTGAGAGTACACAGCTACTGTAGAGGCCAAACAAGTGGTCCAGCAGGAGGCCCAGC
AGGCCCAGTTCTTCGTAGAAAAAGCAAAACTAGAACACCAGCAAAAGATTGCCCAGGCCAAGTGTGAAGCTGAGGCTGCT
AAGATGCTTGGGGAAGCACTGAGCAAGAACCCTGGCTACATCAAAATTCACAAGATTAGGCAGCCCAGAACATCTCCAAG
ACAATCACATCATAGAATCATATCTGTCTCACTGATGACAATCTTGTGCTGAACCTACAGGATAAGACTTTCACCTGGGG
AAATAAAGGCAGCCTCATTAAGGGTAAGAAA

Alignment

ORF - retro_hsap_624 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.35 %
• Parental protein coverage: 83.95 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AIFFNRIGGVQQDTILAEG-LHFRIPWFQYPIIYDIRARPRKISSPTGSKDLQMVNISLRVLSRPNAQEL
          AIFFN.IGG.QQDTILA.G.LHFRIPW..YPI..DI.A.P.KISS.TGSKDLQMVNISL...S.PN.QEL
Retrocopy AIFFNYIGGMQQDTILAKG<LHFRIPWSRYPINDDILAGP*KISSLTGSKDLQMVNISLYMVSQPNVQEL

Parental  PSMYQRLGLDYEERVLPSIVNEVLKSVVAKFNASQLITQRAQVSLLIRRELTERAKDFSLILDDVAITEL
          PSM...LGLD..E.VLPSIV..VLKSVVAKFNAS.LITQ.AQVSLLI..EL.ERAKDFSLILDDVAITEL
Retrocopy PSMHKHLGLDNKE*VLPSIVKRVLKSVVAKFNAS*LITQWAQVSLLIHWELPERAKDFSLILDDVAITEL

Parental  SFSREYTAAVEAKQVAQQEAQRAQFLVEKAKQEQRQKIVQAEGEAEAAKMLGEALSKNPGYIKLRKIR-A
          SFS.EYTA.VEAKQV.QQEAQ.AQF.VEKAK.E..QKI.QA..EAEAAKMLGEALSKNPGYIK..KIR.A
Retrocopy SFS*EYTATVEAKQVVQQEAQQAQFFVEKAKLEHQQKIAQAKCEAEAAKMLGEALSKNPGYIKIHKIR<A

Parental  AQNISKTIATSQNRIYLTADNLVLNLQDESFTRGS-DSLIKGKK
          AQNISKTI.TS.N.I.LT.DNLVLNLQD..FT.G...SLIKGKK
Retrocopy AQNISKTI-TS*NHICLTDDNLVLNLQDKTFTWGNKGSLIKGKK

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
bodymap2_adipose	0.00 RPM	91.00 RPM
bodymap2_adrenal	0.00 RPM	103.82 RPM
bodymap2_brain	0.00 RPM	42.78 RPM
bodymap2_breast	0.00 RPM	80.64 RPM
bodymap2_colon	0.00 RPM	114.95 RPM
bodymap2_heart	0.00 RPM	58.87 RPM
bodymap2_kidney	0.00 RPM	71.70 RPM
bodymap2_liver	0.00 RPM	87.09 RPM
bodymap2_lung	0.00 RPM	82.81 RPM
bodymap2_lymph_node	0.00 RPM	101.05 RPM
bodymap2_ovary	0.00 RPM	132.20 RPM
bodymap2_prostate	0.00 RPM	168.84 RPM
bodymap2_skeletal_muscle	0.00 RPM	84.74 RPM
bodymap2_testis	0.00 RPM	52.73 RPM
bodymap2_thyroid	0.00 RPM	87.30 RPM
bodymap2_white_blood_cells	0.00 RPM	120.33 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_624 was not detected

EST

1 EST(s) were mapped to retro_hsap_624 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA707822	111288224	111288507	99.7	281	1	279

TSS

No TSS is located nearby retro_hsap_624 retrocopy 5' end.

Lab

retro_hsap_624 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_624 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_557

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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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).