RetrogeneDB ID: retro_hsap_1388

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 14:20992447..20993158(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000258456
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PTCD2
• Ensembl ID: ENSG00000049883
• Aliases: None
• Description: pentatricopeptide repeat domain 2 [Source:HGNC Symbol;Acc:25734]

Sequence

>retro_hsap_1388
CTCATGAAAGACCAGCATTTATGAGATTCCTTCTCAGATTCCACATCATTCAATATTTTGATGGATATGTTATTTATCAA
AGGCAAATATAAAAGTGCTTTGGAAGTATTGATAGAGATGAAAAATCAAGCTGTGAAATTCACCAAATATCCTATGTTCT
TAGTTTTGCAGTTTGCAACAAACTGAAGAGCGCTGAGTCTTTCAAAATCTGTTCTGCATTAACAGAAGAAGCCCCACTCA
AAGGAGAGGTTCCCTCCAGGAGAGCATCCCGTTTCTTTGTGGCGTTAGCTCTGAATCAGAACCAAGTGGCAAAAGCTATG
TCCATTTTTTTCTCAAACCATGAATCCAGAAAGCATAGCCTGCACTAACTTAACTATTATAATCCATATCCAGTCAAATA
TGTTGGAAACCCTGATAGAGACACTAAAAAAATGCTGCAGAAGGAAATTTATTAAAATTTGTGAAAAGACATGCATTCTC
AGAGGAAGTGCTGGCAAAAGTGAAGGAAAAGTGAAGGATATGCCTGCCCTTGTGGCCAGATTTAATGAGATCTATGGAAA
ACTGCACATCAGTGGCCAGGTCACCACTTGTACTTTGGGTACTCTGCTCTGCCACACCCCCAGGGACAGGAAATCCCATA
TGTTGCTATTAAACAAGAGGATGATGAGCCATTGGACCTTCCAGCCACTCAACCGGTCCTTTTTGGCTGAG

Alignment

ORF - retro_hsap_1388 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.42 %
• Parental protein coverage: 61.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LMKDQHLRGFFSDSTSFNILMDMLFIKGKYKSALQVLIEMKNQDVKFTKD-TYVLAFAICYKLNSPESFK
          LMKDQHL...FSDSTSFNILMDMLFIKGKYKSAL.VLIEMKNQ.VKFTK...YVL.FA.C.KL.S.ESFK
Retrocopy LMKDQHL*DSFSDSTSFNILMDMLFIKGKYKSALEVLIEMKNQAVKFTKY<SYVLSFAVCNKLKSAESFK

Parental  ICTTLREEALLKGEILSRRASCFAVALALNQNEMAKAVSIF-SQIMNPESIACINLNIIIHIQSNMLENL
          IC..L.EEA.LKGE..SRRAS.F.VALALNQN..AKA.SIF.SQ.MNPESIAC.NL.IIIHIQSNMLE.L
Retrocopy ICSALTEEAPLKGEVPSRRASRFFVALALNQNQVAKAMSIF>SQTMNPESIACTNLTIIIHIQSNMLETL

Parental  IKTL-KNAAEGNLSKFVKRHVFSEEVLAKVRE-KVKDVPALVAKFDEIYGTLHITGQVTTDSLDAVLCHT
          I.TL.KNAAEGNL.KFVKRH.FSEEVLAKV.E.KVKD.PALVA.F.EIYG.LHI.GQVTT..L...LCHT
Retrocopy IETL>KNAAEGNLLKFVKRHAFSEEVLAKVKE<KVKDMPALVARFNEIYGKLHISGQVTTCTLGTLLCHT

Parental  PRDRKSHTLLLNKRMVSRRTFQPLSQSLLAE
          PRDRKSH.LLLNKRM.S..TFQPL..S.LAE
Retrocopy PRDRKSHMLLLNKRMMSHWTFQPLNRSFLAE

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	3.50 RPM
bodymap2_adrenal	0.00 RPM	3.89 RPM
bodymap2_brain	0.00 RPM	6.75 RPM
bodymap2_breast	0.00 RPM	7.18 RPM
bodymap2_colon	0.00 RPM	4.85 RPM
bodymap2_heart	0.00 RPM	8.33 RPM
bodymap2_kidney	0.00 RPM	8.13 RPM
bodymap2_liver	0.00 RPM	4.18 RPM
bodymap2_lung	0.00 RPM	1.65 RPM
bodymap2_lymph_node	0.00 RPM	2.98 RPM
bodymap2_ovary	0.00 RPM	7.06 RPM
bodymap2_prostate	0.00 RPM	10.69 RPM
bodymap2_skeletal_muscle	0.00 RPM	5.15 RPM
bodymap2_testis	0.02 RPM	6.66 RPM
bodymap2_thyroid	0.00 RPM	7.44 RPM
bodymap2_white_blood_cells	0.00 RPM	3.17 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1388 was not detected

EST

No EST(s) were mapped for retro_hsap_1388 retrocopy.

TSS

No TSS is located nearby retro_hsap_1388 retrocopy 5' end.

Lab

retro_hsap_1388 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1388 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_952

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016364	1 retrocopy	retro_cjac_1598,
Homo sapiens	ENSG00000049883	2 retrocopies	retro_hsap_1388 , retro_hsap_607,
Gorilla gorilla	ENSGGOG00000010695	2 retrocopies	retro_ggor_1077, retro_ggor_534,
Macaca mulatta	ENSMMUG00000017908	1 retrocopy	retro_mmul_2240,
Nomascus leucogenys	ENSNLEG00000004516	2 retrocopies	retro_nleu_2954, retro_nleu_436,
Otolemur garnettii	ENSOGAG00000008390	1 retrocopy	retro_ogar_3169,
Pan troglodytes	ENSPTRG00000016968	2 retrocopies	retro_ptro_447, retro_ptro_952,
Ictidomys tridecemlineatus	ENSSTOG00000006596	1 retrocopy	retro_itri_1469,

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	0.03 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	0.02 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).