RetrogeneDB ID: retro_hsap_2047

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 19:28296334..28296933(-)
• Located in intron of: ENSG00000267575

Retrocopy information

• Ensembl ID: ENSG00000267323
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC25A1
• Ensembl ID: ENSG00000268928
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1 [Source:HGNC Symbol;Acc:10979]

Sequence

>retro_hsap_2047
TTCCTCAGCAACCAGATGCGGGATGCCCAGGGACTGGTGAACAGCAAGGCGGGCAGCGGTGCGGCCAGTGAGCTAGCGTG
GCCGAGGCCGTGGTGGTCCTATGTCCCATGGAGACCATCAAGGTGAAGTTAATCCATGGCCAGACCTCTCCAAATCCAAG
TACAGGGGATTCTTCCACAGGGTTAGGAGATTGTGCGGGAACACCGGGACTTACCGGGGCCCCACAGGCCCCGTGCTGAA
GCAGGGCTGGAACCAGGCAACTTGTTTCTTTGTCCTGACATCCCTGCGCAGCTGGTACCGAGTGGACAGCCCCAACAAAC
TCATGAACCCGCTGGTCGCTGGGTTCTTCGGAGCCATTGTGGGAGCGGCCAGTGTCTTCGGAAATGCTCCTCTGCACGAG
ATCGAGCCCCAGATGCGAGACCTGGAGGTGCACAAATGCAGAACACATGGGACTGTGGCTGCAAATCCTGAGGGAAGGGC
ACAAGACCTTCTACAAGGGCACTATTGCCTGCCTGGGCCGGGTCTGCCTGCATGTGGCCATAGTGTTTATCATCTATGAT
GAGGTGAGGAAGCTGCTCAACAAAGTGTGGAAGACAGAG

Alignment

ORF - retro_hsap_2047 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.38 %
• Parental protein coverage: 65.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FLSNHMRDAQGRLDSTRGL-LCGLGAGVAEAVVVVCPMETIKVKFIHDQTSPNP-KYRGFFHGVREIVRE
          FLSN.MRDAQG...S..G...CG..A.VAEAVVV.CPMETIKVK.IH.QTSPNP.KYRGFFH.VR.....
Retrocopy FLSNQMRDAQGLVNSKAGS<RCGQ*ASVAEAVVVLCPMETIKVKLIHGQTSPNP<KYRGFFHRVRRLC--

Parental  QGLKGTYQGLTATVLKQGSNQAIRFFVMTSLRNWYRGDNPNKPMNPLITGVFGAIAGAASVFGNTPLDVI
          .G..GTY.G.T..VLKQG.NQA..FFV.TSLR.WYR.D.PNK.MNPL..G.FGAI.GAASVFGN.PL..I
Retrocopy -GNTGTYRGPTGPVLKQGWNQATCFFVLTSLRSWYRVDSPNKLMNPLVAGFFGAIVGAASVFGNAPLHEI

Parental  KTRMQGLEAHKYR-NTWDCG-LQILKKEGLKAFYKGTVPRLGRVCLDVAIVFVIYDEVVKLLNKVWKTD
          ...M..LE.HK.R.NTWDCG.LQIL..EG.K.FYKGT...LGRVCL.VAIVF.IYDEV.KLLNKVWKT.
Retrocopy EPQMRDLEVHKCR<NTWDCG<LQIL-REGHKTFYKGTIACLGRVCLHVAIVFIIYDEVRKLLNKVWKTE

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	0.40 RPM	0.00 RPM
bodymap2_adrenal	0.74 RPM	0.00 RPM
bodymap2_brain	0.19 RPM	0.00 RPM
bodymap2_breast	0.47 RPM	0.00 RPM
bodymap2_colon	1.80 RPM	0.00 RPM
bodymap2_heart	0.90 RPM	0.00 RPM
bodymap2_kidney	1.37 RPM	0.00 RPM
bodymap2_liver	0.11 RPM	0.00 RPM
bodymap2_lung	0.84 RPM	0.00 RPM
bodymap2_lymph_node	2.01 RPM	0.00 RPM
bodymap2_ovary	0.75 RPM	0.00 RPM
bodymap2_prostate	1.54 RPM	0.00 RPM
bodymap2_skeletal_muscle	0.11 RPM	0.00 RPM
bodymap2_testis	0.64 RPM	0.00 RPM
bodymap2_thyroid	1.07 RPM	0.00 RPM
bodymap2_white_blood_cells	1.38 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_2047 was not detected

EST

No EST(s) were mapped for retro_hsap_2047 retrocopy.

TSS

No TSS is located nearby retro_hsap_2047 retrocopy 5' end.

Lab

retro_hsap_2047 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2047 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1364

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000268928	1 retrocopy	retro_hsap_2047 ,