RetrogeneDB ID: retro_hsap_2371

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 2:203200740..203201450(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000226261
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAM64A
• Ensembl ID: ENSG00000129195
• Aliases: FAM64A, CATS, RCS1
• Description: family with sequence similarity 64, member A [Source:HGNC Symbol;Acc:25483]

Sequence

>retro_hsap_2371
ATGGCTTCTTGGTGGCAGAGAATGGGGACCTCCGTGCACCGGAGATGTCTCCAGCACCAGGAGCAGCTGGAGGATGCAAG
GAGCTGCAGCCCGTGACCAGCCATCAGGAGAACTCCGCGGGTCCCTGGGGTCCCTGTGCAGACAGTTCCAATGGAGGCTG
CCTCTGAGAGCCATCAACCTCAACTTCCGTGCAGGCCCTTCCTGCAAATGCTTGGAAACCCCAGAGCCAGGGCAGCAGGG
CCTCCAGGCTACGGCTCACTCAGCTAAGAGTGCCTTGGGTGCCATGTCCCAGAGAATCCAGGAGTCCTGCCAAAGTGGCA
CCAAGTGGCTGGTGGAGACCCAGGTGAAGGCCAGGAGGAGGAAGAGACGGGCACAGAAGGGCAGTGGCTCCCCAGCTCAC
AGCCTGAGCCAGAAGAGCACCCGGCTATCTGGAGATGCCCCTGCCCACTCAGCCCACAGACCCCTGGGAGAAGGAGCATA
ACTGCCTCTCCGCCCGGATAGGCTCCCATGCCTACCCATTATGACAGTCGATGCAGGAGGCTGCCTTCTGGAGCCCCTAC
TCCTCAACAGAGCCACTCTGCTCTCCCAGCCAGTCTGGCAGTGACCTAGAGCCTATGGGGGTGGGAATTCAGCATCTCCA
GAAGCTGTCCCAAGAGCTAGATGAAGCCATTATGGCGGAAGAGAGTGGTGACATCATCTCTCTCATTCAT

Alignment

ORF - retro_hsap_2371 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.75 %
• Parental protein coverage: 99.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MASRWQNMGTSVRRRSLQHQEQLEDS-KELQPVVSHQETSVG-ALGSLCRQFQRRLPLRAVNLNLRAGPS
          MAS.WQ.MGTSV.RR.LQHQEQLED..KELQPV.SHQE.S.G..LGSLCRQFQ.RLPLRA.NLN.RAGPS
Retrocopy MASWWQRMGTSVHRRCLQHQEQLEDA<KELQPVTSHQENSAG<SLGSLCRQFQWRLPLRAINLNFRAGPS

Parental  WKRLETPEPGQQGLQAAARSAKSALGAVSQRIQESCQSGTKWLVETQVKARRRKRGAQKGSGSPTHSLSQ
          .K.LETPEPGQQGLQA.A.SAKSALGA.SQRIQESCQSGTKWLVETQVKARRRKR.AQKGSGSP.HSLSQ
Retrocopy CKCLETPEPGQQGLQATAHSAKSALGAMSQRIQESCQSGTKWLVETQVKARRRKRRAQKGSGSPAHSLSQ

Parental  KSTRLSGAAPAHSA-ADPWEKEHHRLSVRMGSHAHPLRRSRREAAFRSPYSSTEPLCSPSESDSDLEPVG
          KSTRLSG.APAHSA..DPWEKEH..LS.R.GSHA.PL..S..EAAF.SPYSSTEPLCSPS.S.SDLEP.G
Retrocopy KSTRLSGDAPAHSA>TDPWEKEHNCLSARIGSHAYPL*QSMQEAAFWSPYSSTEPLCSPSQSGSDLEPMG

Parental  AGIQHLQKLSQELDEAIMAEESGDIVSLIH
          .GIQHLQKLSQELDEAIMAEESGDI.SLIH
Retrocopy VGIQHLQKLSQELDEAIMAEESGDIISLIH

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	0.10 RPM
bodymap2_adrenal	0.12 RPM	0.10 RPM
bodymap2_brain	0.05 RPM	0.12 RPM
bodymap2_breast	0.14 RPM	0.08 RPM
bodymap2_colon	0.00 RPM	0.17 RPM
bodymap2_heart	0.00 RPM	0.09 RPM
bodymap2_kidney	0.00 RPM	0.02 RPM
bodymap2_liver	0.02 RPM	0.00 RPM
bodymap2_lung	0.00 RPM	0.11 RPM
bodymap2_lymph_node	0.18 RPM	0.09 RPM
bodymap2_ovary	0.04 RPM	0.73 RPM
bodymap2_prostate	0.00 RPM	0.12 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.11 RPM
bodymap2_testis	0.11 RPM	0.38 RPM
bodymap2_thyroid	0.09 RPM	0.38 RPM
bodymap2_white_blood_cells	0.00 RPM	0.10 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2371 was not detected

EST

No EST(s) were mapped for retro_hsap_2371 retrocopy.

TSS

No TSS is located nearby retro_hsap_2371 retrocopy 5' end.

Lab

retro_hsap_2371 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2371 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1734
Gorilla gorilla	retro_ggor_1801
Pongo abelii	retro_pabe_2141
Macaca mulatta	retro_mmul_959

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006997	1 retrocopy	retro_amel_1136,
Homo sapiens	ENSG00000129195	3 retrocopies	retro_hsap_2371 , retro_hsap_3030, retro_hsap_3071,
Gorilla gorilla	ENSGGOG00000012309	3 retrocopies	retro_ggor_1801, retro_ggor_2091, retro_ggor_2109,
Macaca mulatta	ENSMMUG00000017760	3 retrocopies	retro_mmul_1778, retro_mmul_1935, retro_mmul_959,
Mus musculus	ENSMUSG00000020808	1 retrocopy	retro_mmus_3385,
Nomascus leucogenys	ENSNLEG00000009164	3 retrocopies	retro_nleu_361, retro_nleu_725, retro_nleu_843,
Otolemur garnettii	ENSOGAG00000027433	1 retrocopy	retro_ogar_1490,
Pongo abelii	ENSPPYG00000007877	3 retrocopies	retro_pabe_2141, retro_pabe_2509, retro_pabe_2545,
Pan troglodytes	ENSPTRG00000008641	3 retrocopies	retro_ptro_1734, retro_ptro_2044, retro_ptro_2070,
Rattus norvegicus	ENSRNOG00000008040	1 retrocopy	retro_rnor_1325,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.21 RPM
CEU_NA11843	0.28 RPM
CEU_NA11930	0.26 RPM
CEU_NA12004	0.08 RPM
CEU_NA12400	0.11 RPM
CEU_NA12751	0.17 RPM
CEU_NA12760	0.18 RPM
CEU_NA12827	0.38 RPM
CEU_NA12872	0.14 RPM
CEU_NA12873	0.06 RPM
FIN_HG00183	0.30 RPM
FIN_HG00277	0.30 RPM
FIN_HG00315	0.22 RPM
FIN_HG00321	0.12 RPM
FIN_HG00328	0.31 RPM
FIN_HG00338	0.13 RPM
FIN_HG00349	0.14 RPM
FIN_HG00375	0.10 RPM
FIN_HG00377	0.28 RPM
FIN_HG00378	0.19 RPM
GBR_HG00099	0.20 RPM
GBR_HG00111	0.45 RPM
GBR_HG00114	0.29 RPM
GBR_HG00119	0.24 RPM
GBR_HG00131	0.60 RPM
GBR_HG00133	0.53 RPM
GBR_HG00134	0.41 RPM
GBR_HG00137	0.74 RPM
GBR_HG00142	0.25 RPM
GBR_HG00143	0.26 RPM
TSI_NA20512	0.23 RPM
TSI_NA20513	0.44 RPM
TSI_NA20518	0.22 RPM
TSI_NA20532	0.58 RPM
TSI_NA20538	0.09 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.60 RPM
TSI_NA20771	0.14 RPM
TSI_NA20786	0.10 RPM
TSI_NA20798	0.22 RPM
YRI_NA18870	0.10 RPM
YRI_NA18907	0.31 RPM
YRI_NA18916	0.23 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.08 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.15 RPM
YRI_NA19213	0.02 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.22 RPM

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Indel association:

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