RetrogeneDB ID: retro_hsap_2431

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 20:47751016..47751550(+)
• Located in intron of: ENSG00000124214

Retrocopy information

• Ensembl ID: ENSG00000226284
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARPC3
• Ensembl ID: ENSG00000111229
• Aliases: ARPC3, ARC21, p21-Arc
• Description: actin related protein 2/3 complex, subunit 3, 21kDa [Source:HGNC Symbol;Acc:706]

Sequence

>retro_hsap_2431
ATGCCGGCTCATTACTCTTCTCTCATGGATCCTGACACCAAACTCATCGGAAACATAGCACTGTTACCTATCAGAAGTCA
ATTCAAAGGACCTGCCCCCAGAGAGACAAAAGATACAGATATTGTGGATGAAGCCAACTATTACTTCAAGGCCAATGTCT
TCTTCAAAAACTATGAAATTAAGAATGAAGCTGATAGGACCTTGATATATTTAACTCTCTACATTTCTGAATGTCTGAAA
AAACTCCAAAAGTGCAATTCCAAAAGTCAAGGTGAGAAAGAAATGTATACACTGGGAATCATTAGTTTTCCCATTCCTGG
AGAGCCTGGTTTTCCACTTCACGCAATTTATACCAAACCTGCAAACAAACAGGAAGATGAAGTGATGAGAGCCTATTTAC
AACAGCTAAGGCAAGAGACTGGACTGAGACTTTGTGAGGAAGTTTTCGACCCTAAGAATGATAAACCCAGCACGTGGTGG
ACTTGCTTTGTGAAGAGACAGTTCATGAACAAGAGTCTTTCAGGACCTGGACAG

Alignment

ORF - retro_hsap_2431 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.26 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPAYHSSLMDPDTKLIGNMALLPIRSQFKGPAPRETKDTDIVDEAIYYFKANVFFKNYEIKNEADRTLIY
          MPA..SSLMDPDTKLIGN.ALLPIRSQFKGPAPRETKDTDIVDEA.YYFKANVFFKNYEIKNEADRTLIY
Retrocopy MPAHYSSLMDPDTKLIGNIALLPIRSQFKGPAPRETKDTDIVDEANYYFKANVFFKNYEIKNEADRTLIY

Parental  ITLYISECLKKLQKCNSKSQGEKEMYTLGITNFPIPGEPGFPLNAIYAKPANKQEDEVMRAYLQQLRQET
          .TLYISECLKKLQKCNSKSQGEKEMYTLGI..FPIPGEPGFPL.AIY.KPANKQEDEVMRAYLQQLRQET
Retrocopy LTLYISECLKKLQKCNSKSQGEKEMYTLGIISFPIPGEPGFPLHAIYTKPANKQEDEVMRAYLQQLRQET

Parental  GLRLCEKVFDPQNDKPSKWWTCFVKRQFMNKSLSGPGQ
          GLRLCE.VFDP.NDKPS.WWTCFVKRQFMNKSLSGPGQ
Retrocopy GLRLCEEVFDPKNDKPSTWWTCFVKRQFMNKSLSGPGQ

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	0.16 RPM	84.30 RPM
bodymap2_adrenal	0.43 RPM	161.73 RPM
bodymap2_brain	0.09 RPM	52.06 RPM
bodymap2_breast	0.12 RPM	65.31 RPM
bodymap2_colon	0.15 RPM	77.56 RPM
bodymap2_heart	0.13 RPM	45.84 RPM
bodymap2_kidney	0.06 RPM	118.87 RPM
bodymap2_liver	0.06 RPM	78.03 RPM
bodymap2_lung	0.35 RPM	150.05 RPM
bodymap2_lymph_node	0.18 RPM	137.18 RPM
bodymap2_ovary	0.17 RPM	62.50 RPM
bodymap2_prostate	0.00 RPM	107.37 RPM
bodymap2_skeletal_muscle	0.00 RPM	36.03 RPM
bodymap2_testis	0.26 RPM	84.03 RPM
bodymap2_thyroid	0.28 RPM	80.77 RPM
bodymap2_white_blood_cells	0.32 RPM	397.42 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2431 was not detected

EST

No EST(s) were mapped for retro_hsap_2431 retrocopy.

TSS

No TSS is located nearby retro_hsap_2431 retrocopy 5' end.

Lab

retro_hsap_2431 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2431 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_1790

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008456	1 retrocopy	retro_cfam_11,
Callithrix jacchus	ENSCJAG00000009360	1 retrocopy	retro_cjac_242,
Echinops telfairi	ENSETEG00000006992	2 retrocopies	retro_etel_116, retro_etel_1323,
Felis catus	ENSFCAG00000004132	2 retrocopies	retro_fcat_1048, retro_fcat_73,
Homo sapiens	ENSG00000111229	5 retrocopies	retro_hsap_2431 , retro_hsap_303, retro_hsap_3425, retro_hsap_892, retro_hsap_918,
Microcebus murinus	ENSMICG00000005485	2 retrocopies	retro_mmur_1009, retro_mmur_1507,
Monodelphis domestica	ENSMODG00000011628	1 retrocopy	retro_mdom_71,
Mustela putorius furo	ENSMPUG00000002151	2 retrocopies	retro_mputfur_1346, retro_mputfur_1540,
Oryctolagus cuniculus	ENSOCUG00000011908	1 retrocopy	retro_ocun_1252,
Oreochromis niloticus	ENSONIG00000003785	1 retrocopy	retro_onil_18,
Sarcophilus harrisii	ENSSHAG00000014805	3 retrocopies	retro_shar_144, retro_shar_439, retro_shar_576,
Sus scrofa	ENSSSCG00000009821	1 retrocopy	retro_sscr_177,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.24 RPM
CEU_NA11843	0.06 RPM
CEU_NA11930	0.39 RPM
CEU_NA12004	0.11 RPM
CEU_NA12400	0.11 RPM
CEU_NA12751	0.29 RPM
CEU_NA12760	0.13 RPM
CEU_NA12827	0.14 RPM
CEU_NA12872	0.16 RPM
CEU_NA12873	0.19 RPM
FIN_HG00183	0.16 RPM
FIN_HG00277	0.33 RPM
FIN_HG00315	0.06 RPM
FIN_HG00321	0.18 RPM
FIN_HG00328	0.17 RPM
FIN_HG00338	0.21 RPM
FIN_HG00349	0.20 RPM
FIN_HG00375	0.27 RPM
FIN_HG00377	0.13 RPM
FIN_HG00378	0.15 RPM
GBR_HG00099	0.26 RPM
GBR_HG00111	0.13 RPM
GBR_HG00114	0.21 RPM
GBR_HG00119	0.36 RPM
GBR_HG00131	0.11 RPM
GBR_HG00133	0.19 RPM
GBR_HG00134	0.15 RPM
GBR_HG00137	0.36 RPM
GBR_HG00142	0.28 RPM
GBR_HG00143	0.26 RPM
TSI_NA20512	0.20 RPM
TSI_NA20513	0.22 RPM
TSI_NA20518	0.28 RPM
TSI_NA20532	0.20 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.12 RPM
TSI_NA20765	0.23 RPM
TSI_NA20771	0.11 RPM
TSI_NA20786	0.18 RPM
TSI_NA20798	0.22 RPM
YRI_NA18870	0.20 RPM
YRI_NA18907	0.31 RPM
YRI_NA18916	0.19 RPM
YRI_NA19093	0.18 RPM
YRI_NA19099	0.19 RPM
YRI_NA19114	0.13 RPM
YRI_NA19118	0.23 RPM
YRI_NA19213	0.12 RPM
YRI_NA19214	0.27 RPM
YRI_NA19223	0.40 RPM

---

Indel association:

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