RetrogeneDB ID: retro_hsap_3940

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 8:28096068..28096517(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000253907
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PDLIM7
• Ensembl ID: ENSG00000196923
• Aliases: PDLIM7, LMP1, LMP3
• Description: PDZ and LIM domain 7 (enigma) [Source:HGNC Symbol;Acc:22958]

Sequence

>retro_hsap_3940
GCCTGCATAAAGTGCCTCAGCCTGGGTCTCAGCAGGTCTCAGCCAGTTCAGAGCAAACCACAGGAGGTTCTGGCTCCTGC
CACAAACCCCCTGCAGTTCACGCTTGCACCCAGCACCTTCAACAAGATGGCCTGGCCCTTCAGGGCACCCCCACCACCTG
CTGGCAATGCACCATAGCAGAATGGACAGCTGCTCCAACTGCTGGTCCCAGATGCCACCAAGCAGTGGCTGATGGAGAAC
ACCAAGGACTGGCCACCATGGTCTAGGACAGGCCAGTCACATTCCTTCAGCATCCTTGCCCACGTCATAGACACGGAGTT
CATGCAAGACCTGGATGAGGAACACCTGAAGAAATCAAGGGAAAAGTATGTCCTGGGGCTATAGAGCCCATGCTGACCTG
CCTCCAGGATTGGTACCACCAGCACTCTGCCCACATGCTCAATGTACAG

Alignment

ORF - retro_hsap_3940 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.76 %
• Parental protein coverage: 67.57 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ACGERLSLGLSRAQPVQSKPQKASAPAADPPRYTFAPSVSLNKTARPFGAPPP-ADSAPQQNGQPLRPLV
          AC...LSLGLSR.QPVQSKPQ...APA..P...T.APS...NK.A.PF.APPP.A..AP.QNGQ.L..LV
Retrocopy ACIKCLSLGLSRSQPVQSKPQEVLAPATNPLQFTLAPS-TFNKMAWPFRAPPPPAGNAP*QNGQLLQLLV

Parental  PDASKQRLMENTEDWRPRPGTGQSRSFRILAHLTGTEFMQDPDEEHLKKSREKYVLELQS-PRYTRLRDW
          PDA.KQ.LMENT.DW.P...TGQS.SF.ILAH...TEFMQD.DEEHLKKSREKYVL.L.S.P..T.L.DW
Retrocopy PDATKQWLMENTKDWPPWSRTGQSHSFSILAHVIDTEFMQDLDEEHLKKSREKYVLGL*S<PMLTCLQDW

Parental  HHQRSAHVLNVQ
          .HQ.SAH.LNVQ
Retrocopy YHQHSAHMLNVQ

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	20.65 RPM
bodymap2_adrenal	0.04 RPM	64.74 RPM
bodymap2_brain	0.00 RPM	5.16 RPM
bodymap2_breast	0.00 RPM	25.78 RPM
bodymap2_colon	0.00 RPM	87.11 RPM
bodymap2_heart	0.00 RPM	6.55 RPM
bodymap2_kidney	0.00 RPM	11.75 RPM
bodymap2_liver	0.00 RPM	2.39 RPM
bodymap2_lung	0.00 RPM	28.27 RPM
bodymap2_lymph_node	0.00 RPM	14.66 RPM
bodymap2_ovary	0.00 RPM	68.36 RPM
bodymap2_prostate	0.00 RPM	131.37 RPM
bodymap2_skeletal_muscle	0.00 RPM	32.21 RPM
bodymap2_testis	0.00 RPM	60.18 RPM
bodymap2_thyroid	0.00 RPM	25.03 RPM
bodymap2_white_blood_cells	0.00 RPM	19.59 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3940 was not detected

EST

No EST(s) were mapped for retro_hsap_3940 retrocopy.

TSS

No TSS is located nearby retro_hsap_3940 retrocopy 5' end.

Lab

retro_hsap_3940 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3940 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006678	1 retrocopy	retro_cjac_1124,
Homo sapiens	ENSG00000022267	1 retrocopy	retro_hsap_2878,
Homo sapiens	ENSG00000196923	1 retrocopy	retro_hsap_3940 ,
Macaca mulatta	ENSMMUG00000003146	1 retrocopy	retro_mmul_2283,