RetrogeneDB ID: retro_hsap_1302

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 14:20137138..20138159(+)
• Located in intron of: ENSG00000257493

Retrocopy information

• Ensembl ID: ENSG00000257846
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SSBP3
• Ensembl ID: ENSG00000157216
• Aliases: SSBP3, CSDP, SSDP, SSDP1
• Description: single stranded DNA binding protein 3 [Source:HGNC Symbol;Acc:15674]

Sequence

>retro_hsap_1302
ATCACGTTGGGAGAACAGCCTCGGTTTTTGCACTCGTGGTGGTGTGTATTTTGGGACCTTTACTGTGCAGCTCCTAAAAG
GAGAGACACTTGTGAACATTCAAGTGAAGCAAAAGCCTTTCCTGATTCTAGTGCAGCAGCTGCCCGGAGCCCCGTGCTTG
GCAACATTCCCCCCAACGATGGGATGCCGGGAGGCCGAGTCCCGCCAGGTTTCTTTCAGGGTCCTCCGGGGTCACTGCCC
TCGCCGCATGCACAGCCTCCACCTCACAATCCTAGCAGCATGATGGGACCCCACAGTCAGCCTTTTATGTCACCGCGATA
TGCAGGCGGCCCCAGGCCCCCCGATCAGAATGGGAAACCAGCCTCCTCCGGAGGAGTTCCTGGGAAACAGCCATTGCTGC
CCAATTCCATGGATCCCACACGACAGCAAGGCCACCCCCACATGGGAGGATCAATGCAGAGAATGAACCCTCCCCAAGGC
ATGGGGCCCATGAGTCCCAGCCCACAGAATTACGGCAGTGGCATGAGACCACCACCCAATTCCCTCGGCCCCGCCACGCC
CGGGATTAACATGGGCCCGGGAGCTGGCAGACCCTGGCCCAATCCTAACAGTGCTAACTCAATTCCATACTCCTCCTCAT
CACCTGGTACCTATGTGGGACACCCCCTGGTGGTGGCGGCCCTCCAGGAACACCCACTATGCCCAGTCCCTCAGATTCAA
CAAATTCCAGCGACAACATCTACACAATGATTAATCTGGTGCCACCTGGAGGCAGCCGGTCCAACTTCCTGATGGGTCCC
AGCTTGGACGGTCCAATGGGCAGCATGGGTGGCATGGAGCCACACCACATGAACGGATTGTTAGGGTCAGGCGACATAAA
TGACTTCCAAAAAATTCTCCTAACAACGTGAATAGTATTAGCAATCTTCCAGGCACCCCTCGAGATGACGGCGAGCTAGG
AGGGAACTTCCTCCACTCCTTTCAGAATGACAATTACTCTCCAAGCACGACGATGAGTGTG

Alignment

ORF - retro_hsap_1302 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.99 %
• Parental protein coverage: 87.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ITLGEPPGFLHSWWCVFWDLYCAAPERRDTCEHSSEAKAFHDYSAAAAPSPVLGNIPPNDGMPGGPIPPG
          ITLGE.P.FLHSWWCVFWDLYCAAP.RRDTCEHSSEAKAF.D.SAAAA.SPVLGNIPPNDGMPGG..PPG
Retrocopy ITLGEQPRFLHSWWCVFWDLYCAAPKRRDTCEHSSEAKAFPDSSAAAARSPVLGNIPPNDGMPGGRVPPG

Parental  FFQGPPGSQPSPHAQPPPHNPSSMMGPHSQPFMSPRYAGGPRPP-IRMGNQ-PP-GGVPGTQPLLPNSMD
          FFQGPPGS.PSPHAQPPPHNPSSMMGPHSQPFMSPRYAGGPRPP.IRMGNQ.PP.GGVPG.QPLLPNSMD
Retrocopy FFQGPPGSLPSPHAQPPPHNPSSMMGPHSQPFMSPRYAGGPRPP>IRMGNQPPP<GGVPGKQPLLPNSMD

Parental  PTRQQGHPNMGGSMQRMNPPRGMGPMGPGPQNYGSGMRPPPNSLGPAMPGINMGPGAGRPWPNPNSANSI
          PTRQQGHP.MGGSMQRMNPP.GMGPM.P.PQNYGSGMRPPPNSLGPA.PGINMGPGAGRPWPNPNSANSI
Retrocopy PTRQQGHPHMGGSMQRMNPPQGMGPMSPSPQNYGSGMRPPPNSLGPATPGINMGPGAGRPWPNPNSANSI

Parental  PYSSSSPGTYVG-PPGGG-GPPGTPIMPSPADSTNSSDNIYTMINPVPPGGSRSNFPMGPGSDGPMGGMG
          PYSSSSPGTYVG..P.GG.GPPGTP.MPSP.DSTNSSDNIYTMIN.VPPGGSRSNF.MGP..DGPMG.MG
Retrocopy PYSSSSPGTYVG<TPPGGGGPPGTPTMPSPSDSTNSSDNIYTMINLVPPGGSRSNFLMGPSLDGPMGSMG

Parental  GMEPHHMNGSLGSGDIDG-LPKNSPNNISGISNPPGTPRDDGELGGNFLHSFQNDNYSPSMTMSV
          GMEPHHMNG.LGSGDI...LPKNSPNN...ISN.PGTPRDDGELGGNFLHSFQNDNYSPS.TMSV
Retrocopy GMEPHHMNGLLGSGDIND<LPKNSPNNVNSISNLPGTPRDDGELGGNFLHSFQNDNYSPSTTMSV

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	0.02 RPM	59.08 RPM
bodymap2_adrenal	0.02 RPM	40.02 RPM
bodymap2_brain	0.00 RPM	139.16 RPM
bodymap2_breast	0.10 RPM	46.23 RPM
bodymap2_colon	0.00 RPM	85.29 RPM
bodymap2_heart	0.00 RPM	40.56 RPM
bodymap2_kidney	0.00 RPM	40.43 RPM
bodymap2_liver	0.00 RPM	20.40 RPM
bodymap2_lung	0.00 RPM	59.99 RPM
bodymap2_lymph_node	0.00 RPM	52.79 RPM
bodymap2_ovary	0.04 RPM	150.32 RPM
bodymap2_prostate	0.12 RPM	94.01 RPM
bodymap2_skeletal_muscle	0.00 RPM	38.38 RPM
bodymap2_testis	0.06 RPM	102.73 RPM
bodymap2_thyroid	0.00 RPM	34.97 RPM
bodymap2_white_blood_cells	0.00 RPM	78.44 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1302 was not detected

EST

No EST(s) were mapped for retro_hsap_1302 retrocopy.

TSS

No TSS is located nearby retro_hsap_1302 retrocopy 5' end.

Lab

retro_hsap_1302 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1302 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005029	1 retrocopy	retro_cjac_3827,
Homo sapiens	ENSG00000130511	1 retrocopy	retro_hsap_1911,
Homo sapiens	ENSG00000145687	1 retrocopy	retro_hsap_3622,
Homo sapiens	ENSG00000157216	6 retrocopies	retro_hsap_1302 , retro_hsap_1384, retro_hsap_2155, retro_hsap_2319, retro_hsap_2539, retro_hsap_3721,
Macropus eugenii	ENSMEUG00000009291	1 retrocopy	retro_meug_1372,
Oryctolagus cuniculus	ENSOCUG00000005903	1 retrocopy	retro_ocun_252,
Pan troglodytes	ENSPTRG00000000770	2 retrocopies	retro_ptro_2618, retro_ptro_2931,