RetrogeneDB ID: retro_hsap_1170

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 13:21181656..21182269(+)
• Located in intron of: ENSG00000032742

Retrocopy information

• Ensembl ID: ENSG00000238286
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC35E1
• Ensembl ID: ENSG00000127526
• Aliases: None
• Description: solute carrier family 35, member E1 [Source:HGNC Symbol;Acc:20803]

Sequence

>retro_hsap_1170
GCCGCCACGCTGTGCTTCTTGTTTCAGAACATTTTCTCCAAAAAGATCTTGAGAGATTTGCGGATCCACCATCTCCCGCT
GCTCAACATCTTGGGCTGCCACGCTGTTTTTTTATGATCCCCACCTGGGTTCTGGTGGACCTCTCAGCTTTCCTGGTCAG
CAGCGACTTGACTACGTCTCACAGTGGCCCTGGATGCTCCTGCTTCTGGCTGTCAGCGGCTTCTGTAACTTTGCCTAGAA
TGTCATTGCCTTCAGCATCCTCAACCTCGTCAGCTCTCTGAGCTATTCAGTTGTCAATGCCACCAAGAGAATCATGGTCA
TCACAGTGTCCCTGATCATGCTGCCCAACCCAGTCACCAGCACCAATGTCCTGGGCATAATGACTGCCATCCTCGGGGTC
TTCCTCTACAAGACCAAGTAAGATGCAAACCAGCAAGTCAGGAAGCACCTCCTCCTGGCACCACAGTGGACCTGAGCAGC
AAGGAACATCACCAGAGCCCACTGGAGAAGCCCCACCAATGGCCTCCTCTTCCCCCAGCACGGGGACTATCATGGCTGCA
ACAATATCTTAACAGACCACTTCCAGTACAGCTGGCAGAGCTACCCAAACTCT

Alignment

ORF - retro_hsap_1170 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.2 %
• Parental protein coverage: 50.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  AATLCFSLQNIFSKKVLRDSRIHHLRLLNILGCHAVF-FMIPTWVLVDLSAFLVSSDLT-YVYQWPWTLL
          AATLCF..QNIFSKK.LRD.RIHHL.LLNILGCHAVF.FMIPTWVLVDLSAFLVSSDLT.YV.QWPW.LL
Retrocopy AATLCFLFQNIFSKKILRDLRIHHLPLLNILGCHAVF<FMIPTWVLVDLSAFLVSSDLT<YVSQWPWMLL

Parental  LLAVSGFCNFAQNVIAFSILNLVSPLSYSVANATKRIMVITVSLIMLRNPVTSTNVLGMMTAILGVFLYN
          LLAVSGFCNFA.NVIAFSILNLVS.LSYSV.NATKRIMVITVSLIML.NPVTSTNVLG.MTAILGVFLY.
Retrocopy LLAVSGFCNFA*NVIAFSILNLVSSLSYSVVNATKRIMVITVSLIMLPNPVTSTNVLGIMTAILGVFLY-

Parental  KTKYDANQQARKHLL-PVTTADLSSKERHRSPLEKPH-NGLLFPQHGDYQYGRNNILTDHFQYSRQSYPN
          KTK.DANQQ.RKHLL.P.TT.DLSSKE.H.SPLEKPH.NGLLFPQHGDY..G.NNILTDHFQYS.QSYPN
Retrocopy KTK*DANQQVRKHLL<PGTTVDLSSKEHHQSPLEKPH>NGLLFPQHGDY-HGCNNILTDHFQYSWQSYPN

Parental  S
          S
Retrocopy S

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	72.34 RPM
bodymap2_adrenal	0.18 RPM	49.15 RPM
bodymap2_brain	0.12 RPM	32.39 RPM
bodymap2_breast	0.10 RPM	68.79 RPM
bodymap2_colon	0.04 RPM	50.45 RPM
bodymap2_heart	0.04 RPM	32.18 RPM
bodymap2_kidney	0.12 RPM	46.14 RPM
bodymap2_liver	0.00 RPM	25.96 RPM
bodymap2_lung	0.00 RPM	54.41 RPM
bodymap2_lymph_node	0.00 RPM	45.15 RPM
bodymap2_ovary	0.08 RPM	59.14 RPM
bodymap2_prostate	0.00 RPM	57.54 RPM
bodymap2_skeletal_muscle	0.00 RPM	61.60 RPM
bodymap2_testis	0.11 RPM	34.22 RPM
bodymap2_thyroid	0.28 RPM	52.26 RPM
bodymap2_white_blood_cells	0.00 RPM	62.31 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1170 was not detected

EST

No EST(s) were mapped for retro_hsap_1170 retrocopy.

TSS

No TSS is located nearby retro_hsap_1170 retrocopy 5' end.

Lab

retro_hsap_1170 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1170 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
Homo sapiens	ENSG00000127526	1 retrocopy	retro_hsap_1170 ,
Nomascus leucogenys	ENSNLEG00000005563	1 retrocopy	retro_nleu_2854,
Pongo abelii	ENSPPYG00000009692	1 retrocopy	retro_pabe_981,
Pan troglodytes	ENSPTRG00000010648	1 retrocopy	retro_ptro_804,