RetrogeneDB ID: retro_hsap_3622

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:82973983..82974691(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000220537
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SSBP2
• Ensembl ID: ENSG00000145687
• Aliases: None
• Description: single-stranded DNA binding protein 2 [Source:HGNC Symbol;Acc:15831]

Sequence

>retro_hsap_3622
ATGTACAGCAAAGGCAAGAGTAACAGCAGCATTAACCCATGTGACAGCCACACCTTGGTGAAGTTAGCACTTTACATATA
TGAATATCTGCTCCATGTAGGAGTTCAGAGATCATCCCGAACATTTTTATCAGAGATAAGATGGGGGAAAAAATTGGGAG
AACCACCAGGATTCTTACATTCCTGGTGTTGTGTATTTTGGGATCTCTATTTGGCAGCTCCAGAGCCAAAGGAAACATGT
GAACACTCAAGTGTAACAAAAAACTTCCATGATTATCTTTTTATATCACCTTGGTACCCTGGAGGTCCAAGGTTCCCATT
GAAGATACCTAAAGAGGCACTTGGAAGTATCCTAGGAAGTCAGCCATTACTCCCCAGTGGAATCCAACTTGACAACAAGG
ACATTTAAGTATGGGTGGGCCAATTTCTCCAAGAGGAATGGTGCCCTGAGGGCCACAGTCTGATCCTTGGTTGTCAGTAC
AGAATGATGAAGGTGCAATGAGATGCCCAGTGAATGCTTTAGGTGGCTCTGGAATGCCTAGAATGAACATGGGTCTGGAG
GGTGGCAGATCTTGGCCAAACCCAACAAATGCCAATTCAGTACCATACTCCTCAACATCTCCTGGGAATTACATAGGCCC
TCCAGGAGGTGAGGTCCACAGGAACACCCGTCATGTCTAGTCTAGCAGATTTAATCAACCCTGGAGAT

Alignment

ORF - retro_hsap_3622 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.83 %
• Parental protein coverage: 71.98 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MYGKGKSNSSAVPSDSQAREKLALYVYEYLLHVGAQKSAQTFLSEIRWEKNITLGEPPGFLHSWWCVFWD
          MY.KGKSNSS..P.DS....KLALY.YEYLLHVG.Q.S..TFLSEIRW.K...LGEPPGFLHSW.CVFWD
Retrocopy MYSKGKSNSSINPCDSHTLVKLALYIYEYLLHVGVQRSSRTFLSEIRWGKK--LGEPPGFLHSWCCVFWD

Parental  LYCAAPERRETCEHSSEAKAFHDYPFMSPRYPGGPRPPLRIPNQALGGV-PGSQPLLPSGMDPTRQQGHP
          LY.AAPE..ETCEHSS..K.FHDY.F.SP.YPGGPR.PL.IP..ALG...P......P....PT.QQGH.
Retrocopy LYLAAPEPKETCEHSSVTKNFHDYLFISPWYPGGPRFPLKIPKEALGSI<PRKSAITPQ-WNPT*QQGHL

Parental  NMGGPMQRMTPPRGMVPLGPQSDPWLSLQNYGGAMRPPLNALGGPGMPGMNMGPGGGRPWPNPTNANSIP
          .MGGP......PRGMVP.GPQSDPWLS.QN..GAMR.P.NALGG.GMP.MNMG..GGR.WPNPTNANS.P
Retrocopy SMGGPIS----PRGMVP*GPQSDPWLSVQNDEGAMRCPVNALGGSGMPRMNMGLEGGRSWPNPTNANSVP

Parental  YSSASPGNYVGPPGGG-GP-PGTPIMPSPADSTNSGD
          YSS.SPGNY.GPPGG..GP..GTP.M.S.AD..N.GD
Retrocopy YSSTSPGNYIGPPGGE<GP<TGTPVMSSLADLINPGD

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	41.74 RPM
bodymap2_adrenal	0.00 RPM	27.96 RPM
bodymap2_brain	0.00 RPM	59.16 RPM
bodymap2_breast	0.00 RPM	46.93 RPM
bodymap2_colon	0.00 RPM	55.55 RPM
bodymap2_heart	0.00 RPM	29.57 RPM
bodymap2_kidney	0.00 RPM	25.04 RPM
bodymap2_liver	0.00 RPM	3.76 RPM
bodymap2_lung	0.00 RPM	40.52 RPM
bodymap2_lymph_node	0.00 RPM	38.05 RPM
bodymap2_ovary	0.00 RPM	105.31 RPM
bodymap2_prostate	0.00 RPM	74.15 RPM
bodymap2_skeletal_muscle	0.00 RPM	25.55 RPM
bodymap2_testis	0.02 RPM	46.23 RPM
bodymap2_thyroid	0.00 RPM	36.27 RPM
bodymap2_white_blood_cells	0.00 RPM	39.14 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3622 was not detected

EST

No EST(s) were mapped for retro_hsap_3622 retrocopy.

TSS

No TSS is located nearby retro_hsap_3622 retrocopy 5' end.

Lab

retro_hsap_3622 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3622 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
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,
Macaca mulatta	ENSMMUG00000017583	1 retrocopy	retro_mmul_1768,
Mus musculus	ENSMUSG00000003992	1 retrocopy	retro_mmus_2353,