RetrogeneDB ID: retro_hsap_4233

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 9:17447145..17448535(-)
• Located in intron of: ENSG00000044459

Retrocopy information

• Ensembl ID: ENSG00000224488
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SAMM50
• Ensembl ID: ENSG00000100347
• Aliases: SAMM50, OMP85, SAM50, TOB55, TRG-3, YNL026W
• Description: sorting and assembly machinery component 50 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:24276]

Sequence

>retro_hsap_4233
ACATTGTACACGCAGAGTTTGGAGCCTCTTCCACCAAGAGGATCTGGCTTTGGAGCATCAGAAAATGAAACTGAATTTGC
TGAAGGTGAAAGTGAAGCTAAACAGGAAATTCTTAAAAACAAAGATCTGGCTGTTCAACATGCCCATTTTTATGGGCTTG
GATGGACTAAATAAAGATAATATCACCGTTTGTAAAACTGGAGATGTTTTTAAGGCTAAAAATCTCATTGAGGTAATGTG
GAATTCTCATGAAGCCCGTGAAAAATTTCTTCATCCAGGAATTTTTTAGACAAGTGAATTTTTTGAGTGATACATGTCAA
GGTGACAATGCATTTCCAAATGGGTTAGATGTTACCTTTGAAGTAACTGAATTAAGGAAATTAATGGGCAGTTAAAACAC
CATGGTTGGAAACAATGAAGGGAGTACGGTACTTGGCCTCAAACTCCCTGATCTTCTAGGTTATGCAGAAAAGGCGACTT
TTCATTTTTCCCATGGAACAAAAGACGCTTCCCATGGCCTTTCTTCAAACCATGGCCCGGAAACTTCAAAAGGAATTTAT
CTGTAAACTTACATGAAGTTACTGAACAGTTCCCTTGGAGCTCACTTCCGGAAATGAACAGAAGATGATCAGCCAAGTAC
AGTCTTCCCATATGAAAGACCAGCCACACCAACAATTGGAAAGGCATGTGGCGAGACCTGGGCTGTCACTTAAGGACAGC
ATCATTTGCTGTTTGAAAGTAAGGCAGACATTCACTTAAATCATGTCTTTCACATGCCATGGTCATCGATTTTCAGAATT
CTTCCATCTTACCAAGAAAATGTGTTTTGCTGAAAGTTAACCAGGAACTGACAGGCTACACTACAAGGGATATAAGCTTC
ATCAAAGATTTTGAACTTCAGTTGAATAAACCACTCATATTTGATTCAGTTTTTTCAGCAATTCTCTGAGGTGGGATGTT
GGCACCCATGGTGATAAACTGTGAGTCCTGCTGATAGTTTCACCTTGGGGGACCAACAAGTGTCCAAGGATTCAGCATGC
ACAGCACCGGAGCAGAGTGCAGGCGACCACCTAGGTGGAGAAGCACGCTGGGCCAGCGGACCGCAACTGTGTACGCCAAC
ACGTTTAAAGCCAAGCCAGGGCAGTTTGGGAGAACTTTTCCAAACACTTTTTTCTCAACACAGGAAACCTCTGCAACCTC
AACTATGGGGAGGGCCCCAAAGTGTATTCGTGAGCTGGCTGAATGTATCTGCCAGTTTTATGGCACCAGGATTGTCTTTA
GGCTTGGCAACATGGCTCTGTTGGAACTTAATTACTACTTTCCTATGGGAGTGCAGACAGGCAACAGGATATGTGATAGC
ATCTAGTTTTGAGCTGGGATAAGGTTCCTG

Alignment

ORF - retro_hsap_4233 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.76 %
• Parental protein coverage: 99.57 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  TVHARSLEPLPSSGPDFGGLGEEAEFVEVEPEAKQEILENKDVVVQHVH-FDGL-GRTKDDIIICEIGDV
          T....SLEPLP..G..FG....E.EF.E.E.EAKQEIL.NKD..VQH.H.F.GL.G..KD.I..C..GDV
Retrocopy TLYTQSLEPLPPRGSGFGASENETEFAEGESEAKQEILKNKDLAVQHAH>FMGLDGLNKDNITVCKTGDV

Parental  FKAKNLIEVMRKSHEAREKLLRLGIF-RQVDVLIDTCQGDDALPNGLDVTFEVTELRRLTGSYNTMVGNN
          FKAKNLIEVM..SHEAREK.L..GIF.RQV..L.DTCQGD.A.PNGLDVTFEVTELR.L.GS.NTMVGNN
Retrocopy FKAKNLIEVMWNSHEAREKFLHPGIF>RQVNFLSDTCQGDNAFPNGLDVTFEVTELRKLMGS*NTMVGNN

Parental  EGSMVLGLKLPNLLGRAEKVT-FQFSYGTKETSYGLSFFKPRPGNFERNFSVNLYKVTGQFPWSSLRETD
          EGS.VLGLKLP.LLG.AEK.T.F.F............FFKP.PGNF.RN.SVNL..VT.QFPWSSL.E..
Retrocopy EGSTVLGLKLPDLLGYAEKAT<FSF-FPWNKRRFPWPFFKPWPGNFKRNLSVNLHEVTEQFPWSSLPEMN

Parental  RGMSAEYSFPIWKTSHTVKWEGVWRELGCLSRTASFAVRKESGHSLKSSLSHAMVIDSRNSSILPRRGAL
          R..SA.YS.PI.KTSHT..W.G.WR.LGC..RTASFAV.K...HSLKS.LSHAMVID..NSSILPR...L
Retrocopy RR*SAKYSLPI*KTSHTNNWKGMWRDLGCHLRTASFAV*K*GRHSLKSCLSHAMVIDFQNSSILPRKCVL

Parental  LKVNQELAGYTGGDVSFIKEDFELQLNKQLIFDSVFSASFWGGMLVPI-GDK-PSSIADRFYLGGPTSIR
          LKVNQEL.GYT..D.SFIK.DFELQLNK.LIFDSVFSA...GGML.P..GDK...S.AD.F.L.G.....
Retrocopy LKVNQELTGYTTRDISFIK-DFELQLNKPLIFDSVFSAIL*GGMLAPM<GDK<TVSPADSFTL-GDQQVS

Parental  GFSMHSIGPQSEGDYLGGEAYWAGGLHLYTPLPFRPGQGG-FG-ELFRTHFFLNAGNLCNLNYGEG-PKA
          ..S......QS.GD.LGGEA.WA.G..L.TP....P.QG..FG.E.F..HFFLN.GNLCNLNYGEG.PK.
Retrocopy KDSACTAPEQSAGDHLGGEARWASGPQLCTPTRLKPSQGS<FG<ENFSKHFFLNTGNLCNLNYGEG>PKC

Parental  HIRKLAECIRWSYGAGIVLRLGNIARLELNYCVPMGVQTGDRICDGVQFGAGIRFL
          .IR.LAECI...YG..IV.RLGN.A.LELNY..PMGVQTG.RICD...F.AGIRFL
Retrocopy -IRELAECICQFYGTRIVFRLGNMALLELNYYFPMGVQTGNRICDSI*F*AGIRFL

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	0.10 RPM	87.40 RPM
bodymap2_adrenal	0.00 RPM	43.72 RPM
bodymap2_brain	0.00 RPM	35.30 RPM
bodymap2_breast	0.00 RPM	83.91 RPM
bodymap2_colon	0.00 RPM	39.62 RPM
bodymap2_heart	0.00 RPM	46.30 RPM
bodymap2_kidney	0.00 RPM	35.38 RPM
bodymap2_liver	0.00 RPM	29.61 RPM
bodymap2_lung	0.00 RPM	13.77 RPM
bodymap2_lymph_node	0.00 RPM	25.89 RPM
bodymap2_ovary	0.00 RPM	51.74 RPM
bodymap2_prostate	0.35 RPM	41.97 RPM
bodymap2_skeletal_muscle	0.00 RPM	72.93 RPM
bodymap2_testis	0.00 RPM	52.81 RPM
bodymap2_thyroid	0.00 RPM	46.70 RPM
bodymap2_white_blood_cells	0.00 RPM	38.21 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4233 was not detected

EST

No EST(s) were mapped for retro_hsap_4233 retrocopy.

TSS

No TSS is located nearby retro_hsap_4233 retrocopy 5' end.

Lab

retro_hsap_4233 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4233 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2876
Pongo abelii	retro_pabe_3404
Macaca mulatta	retro_mmul_1152
Callithrix jacchus	retro_cjac_605

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015070	2 retrocopies	retro_cjac_2277, retro_cjac_605,
Homo sapiens	ENSG00000100347	1 retrocopy	retro_hsap_4233 ,
Macaca mulatta	ENSMMUG00000015446	1 retrocopy	retro_mmul_1152,
Nomascus leucogenys	ENSNLEG00000015693	1 retrocopy	retro_nleu_1035,
Pongo abelii	ENSPPYG00000011918	1 retrocopy	retro_pabe_3404,
Pan troglodytes	ENSPTRG00000014483	1 retrocopy	retro_ptro_2876,