RetrogeneDB ID: retro_hsap_3101

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 4:140036086..140036528(-)
• Located in intron of: ENSG00000109381

Retrocopy information

• Ensembl ID: ENSG00000179967
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPP1R14B
• Ensembl ID: ENSG00000173457
• Aliases: PPP1R14B, PHI-1, PLCB3N, PNG, SOM172
• Description: protein phosphatase 1, regulatory (inhibitor) subunit 14B [Source:HGNC Symbol;Acc:9057]

Sequence

>retro_hsap_3101
ATGGCGGACAGCGGCACCGCGGGGGGCGCGGCGTTGGCGACCCCGGCCCCCGGGCCGGGCAGTGGCGGCCCAGGACCACG
CGTCTACTTTCAGAGCCCCCCCCGGGACCGCAGGAGAGGGCCCGGGCGGCGCGGACGATGAGGGCCCAGTGAGGCGCCAA
GGGAAGGTCACCGTCAAGTATGACCGCAAGGAGCTACGGAAGCGCCTCAACCTAGAGGAGTGGATCCTGGAGCAGCTCAC
GCGCCTCTACGACTGCCAGGAAGAGGAGATCCCAGAACTGGAGATTGACGTGGATGAGCTCCTGGACATGGAGAGTGACG
ATGCCCGGGCTGCCACGGTCAAGGAGCTGCTGGTTGACTGTTACAAACCCACAGAGGCCTTCATTTCTGGTCTGCTGGAC
AAGATCCGGGGCATGCAGAAGCTGAGCACACCCCAGAAGAAG

Alignment

ORF - retro_hsap_3101 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.27 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADSGTAGGAALAAPAPGPGSGGPGPRVYFQSPP-GAAGEGPGGADDEGPVRRQGKVTVKYDRKELRKRL
          MADSGTAGGAALA.PAPGPGSGGPGPRVYFQ....G.AGEGPGGADDEGPVRRQGKVTVKYDRKELRKRL
Retrocopy MADSGTAGGAALATPAPGPGSGGPGPRVYFQXXX>GTAGEGPGGADDEGPVRRQGKVTVKYDRKELRKRL

Parental  NLEEWILEQLTRLYDCQEEEIPELEIDVDELLDMESDDARAARVKELLVDCYKPTEAFISGLLDKIRGMQ
          NLEEWILEQLTRLYDCQEEEIPELEIDVDELLDMESDDARAA.VKELLVDCYKPTEAFISGLLDKIRGMQ
Retrocopy NLEEWILEQLTRLYDCQEEEIPELEIDVDELLDMESDDARAATVKELLVDCYKPTEAFISGLLDKIRGMQ

Parental  KLSTPQKK
          KLSTPQKK
Retrocopy KLSTPQKK

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	4.93 RPM	26.60 RPM
bodymap2_adrenal	6.88 RPM	34.20 RPM
bodymap2_brain	0.75 RPM	3.75 RPM
bodymap2_breast	4.69 RPM	20.27 RPM
bodymap2_colon	4.74 RPM	22.35 RPM
bodymap2_heart	2.25 RPM	13.02 RPM
bodymap2_kidney	4.94 RPM	30.55 RPM
bodymap2_liver	3.46 RPM	19.14 RPM
bodymap2_lung	4.54 RPM	18.74 RPM
bodymap2_lymph_node	4.39 RPM	21.00 RPM
bodymap2_ovary	1.97 RPM	20.47 RPM
bodymap2_prostate	4.33 RPM	21.65 RPM
bodymap2_skeletal_muscle	8.42 RPM	50.42 RPM
bodymap2_testis	3.68 RPM	17.33 RPM
bodymap2_thyroid	4.05 RPM	21.19 RPM
bodymap2_white_blood_cells	2.28 RPM	9.04 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3101 was not detected

EST

No EST(s) were mapped for retro_hsap_3101 retrocopy.

TSS

No TSS is located nearby retro_hsap_3101 retrocopy 5' end.

Lab

retro_hsap_3101 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3101 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2097

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018111	3 retrocopies	retro_cjac_3591, retro_cjac_428, retro_cjac_532,
Homo sapiens	ENSG00000173457	4 retrocopies	retro_hsap_2205, retro_hsap_3101 , retro_hsap_3655, retro_hsap_3838,
Mustela putorius furo	ENSMPUG00000013208	2 retrocopies	retro_mputfur_235, retro_mputfur_798,
Nomascus leucogenys	ENSNLEG00000004890	2 retrocopies	retro_nleu_324, retro_nleu_335,
Pan troglodytes	ENSPTRG00000041138	6 retrocopies	retro_ptro_1674, retro_ptro_2097, retro_ptro_2480, retro_ptro_2614, retro_ptro_3089, retro_ptro_935,
Sus scrofa	ENSSSCG00000013035	2 retrocopies	retro_sscr_1087, retro_sscr_892,
Ictidomys tridecemlineatus	ENSSTOG00000021959	1 retrocopy	retro_itri_1110,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	1.18 RPM
CEU_NA11843	1.91 RPM
CEU_NA11930	1.37 RPM
CEU_NA12004	1.63 RPM
CEU_NA12400	1.09 RPM
CEU_NA12751	0.75 RPM
CEU_NA12760	1.75 RPM
CEU_NA12827	1.18 RPM
CEU_NA12872	1.12 RPM
CEU_NA12873	0.86 RPM
FIN_HG00183	1.37 RPM
FIN_HG00277	0.74 RPM
FIN_HG00315	1.27 RPM
FIN_HG00321	1.18 RPM
FIN_HG00328	1.07 RPM
FIN_HG00338	1.11 RPM
FIN_HG00349	1.42 RPM
FIN_HG00375	1.44 RPM
FIN_HG00377	1.66 RPM
FIN_HG00378	0.98 RPM
GBR_HG00099	1.05 RPM
GBR_HG00111	1.42 RPM
GBR_HG00114	1.16 RPM
GBR_HG00119	1.03 RPM
GBR_HG00131	1.12 RPM
GBR_HG00133	1.06 RPM
GBR_HG00134	0.98 RPM
GBR_HG00137	1.62 RPM
GBR_HG00142	1.39 RPM
GBR_HG00143	1.44 RPM
TSI_NA20512	1.95 RPM
TSI_NA20513	1.11 RPM
TSI_NA20518	1.83 RPM
TSI_NA20532	1.19 RPM
TSI_NA20538	1.20 RPM
TSI_NA20756	1.02 RPM
TSI_NA20765	0.97 RPM
TSI_NA20771	1.59 RPM
TSI_NA20786	1.41 RPM
TSI_NA20798	1.25 RPM
YRI_NA18870	1.56 RPM
YRI_NA18907	1.77 RPM
YRI_NA18916	1.03 RPM
YRI_NA19093	0.86 RPM
YRI_NA19099	1.12 RPM
YRI_NA19114	0.73 RPM
YRI_NA19118	0.73 RPM
YRI_NA19213	1.03 RPM
YRI_NA19214	0.64 RPM
YRI_NA19223	1.53 RPM

---

Indel association:

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