RetrogeneDB ID: retro_hsap_2841

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 3:136618300..136618918(-)
• Located in intron of: ENSG00000158092

Retrocopy information

• Ensembl ID: ENSG00000214283
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAD51AP1
• Ensembl ID: ENSG00000111247
• Aliases: RAD51AP1, PIR51
• Description: RAD51 associated protein 1 [Source:HGNC Symbol;Acc:16956]

Sequence

>retro_hsap_2841
ATGGTGCAGCCTGTGAGATGTAAGAAACCAATCAATTACTCACAGTTTGGCGACTCTGACAGTGATGATGATTTTGTTTC
TGCAACTGTACCTTTAAACAAGCAATCCAGAACATCAAAGGAGTTAAAACAAGATAAACCAAAACCTAATTTGAACAATC
TCCAGAAAGAAGAAATCCCACTAGAAGAGAAAACCCCTAAAAAAAAAAGGATGGCTTTAGATGATAAGCTCTACCAGAGA
GACTTAGAAGTTGCACTAGCTTTATCAGTGAAGGAACTTTCAACAGTCACCACTAATGTGCAGAAGTCTCAAGATAAAAG
AGTTGAAAAACATGGCAATAGTAGAACAGAAACAGTGAGTAAGTCTCCTCGTATCTCTAATTGCAGTGTAGCCAGTGATT
ATTTAGATTTGGATAAGATTACTAAGAAAGACAATGGTGGTATTCAAGGGAAAAGAAAAGCAGCATCTAAAGCTGCGGTA
CAACAGAGGAAAATTTTTCTGGAAGGCAGTGATGGCAATAGTGCTAATAACACCAAACCAGACTTGGCAACTGGTGAAGA
TTCTGAGGATGATTCTGATTTTGGTGAGAGTGAGGATAATGACAAAGACTCCTCTATG

Alignment

ORF - retro_hsap_2841 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.77 %
• Parental protein coverage: 61.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVRPVRHKKPVNYSQFDHSDSDDDFVSATVPLNKKSRTAPKELKQDKPKPNLNNLRKEEIPVQEKTPKKR
          MV.PVR.KKP.NYSQF..SDSDDDFVSATVPLNK.SRT..KELKQDKPKPNLNNL.KEEIP..EKTP...
Retrocopy MVQPVRCKKPINYSQFGDSDSDDDFVSATVPLNKQSRTS-KELKQDKPKPNLNNLQKEEIPLEEKTPXXX

Parental  -MALDDKLYQRDLEVALALSVKELPTVTTNVQNSQDKSIEKHGSSKIETMNKSPHISNCSVASDYLDLDK
          .MALDDKLYQRDLEVALALSVKEL.TVTTNVQ.SQDK..EKHG.S..ET..KSP.ISNCSVASDYLDLDK
Retrocopy XMALDDKLYQRDLEVALALSVKELSTVTTNVQKSQDKRVEKHGNSRTETVSKSPRISNCSVASDYLDLDK

Parental  ITVEDDVGGVQGKRKAASKAAAQQRKILLEGSDGDSANDTEPDFAPGEDSEDDSDFCESEDNDEDFSM
          IT..D..GG.QGKRKAASKAA.QQRKI.LEGSDG.SAN.T.PD.A.GEDSEDDSDF.ESEDND.D.SM
Retrocopy ITKKDN-GGIQGKRKAASKAAVQQRKIFLEGSDGNSANNTKPDLATGEDSEDDSDFGESEDNDKDSSM

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	0.78 RPM
bodymap2_adrenal	0.16 RPM	1.74 RPM
bodymap2_brain	0.00 RPM	0.73 RPM
bodymap2_breast	0.00 RPM	1.85 RPM
bodymap2_colon	0.00 RPM	0.62 RPM
bodymap2_heart	0.06 RPM	1.11 RPM
bodymap2_kidney	0.00 RPM	1.18 RPM
bodymap2_liver	0.00 RPM	0.21 RPM
bodymap2_lung	0.00 RPM	0.49 RPM
bodymap2_lymph_node	0.00 RPM	1.37 RPM
bodymap2_ovary	0.00 RPM	0.56 RPM
bodymap2_prostate	0.00 RPM	1.39 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.42 RPM
bodymap2_testis	0.06 RPM	7.32 RPM
bodymap2_thyroid	0.00 RPM	1.36 RPM
bodymap2_white_blood_cells	0.00 RPM	1.83 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_2841 was not detected

EST

No EST(s) were mapped for retro_hsap_2841 retrocopy.

TSS

No TSS is located nearby retro_hsap_2841 retrocopy 5' end.

Lab

retro_hsap_2841 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2841 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
Choloepus hoffmanni	ENSCHOG00000010098	1 retrocopy	retro_chof_2173,
Homo sapiens	ENSG00000111247	1 retrocopy	retro_hsap_2841 ,
Nomascus leucogenys	ENSNLEG00000003178	1 retrocopy	retro_nleu_1595,
Tupaia belangeri	ENSTBEG00000010089	1 retrocopy	retro_tbel_4671,