RetrogeneDB ID: retro_hsap_208

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:113466183..113466960(+)
• Located in intron of: ENSG00000155380

Retrocopy information

• Ensembl ID: ENSG00000229020
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AKR7A3
• Ensembl ID: ENSG00000162482
• Aliases: None
• Description: aldo-keto reductase family 7, member A3 (aflatoxin aldehyde reductase) [Source:HGNC Symbol;Acc:390]

Sequence

>retro_hsap_208
CTGAAAATTGATACCAAGGCCAATCCATTGTTTGGGAACTCCCTGAAACCTGACAGTCTCCGGTTCCAGCTGGAGACGTC
ACTGAAGTGGCTGCAGTGTCCCCGAGTGGACCTCTTCTACCTGCTCAGGCCAGACCACAGCACCCCGGTGGAAGAGACAC
TGAGTGCCTGCCACCAGCTGCACCAGGAGGGCAAGTTCCTGGATCTTGGCCTCTCCAACTATGCCACCTGGGAAGTGGCC
AAGATCTGTAACCTCTGCAAGAGCAATGGCTGGACCCTGCCCACTGTGTACCAGGGCATGTACAACGCCACCACCCAGCA
GGTGAAAACGGAGCTCTTCCCCTGCCTCAGGCACTCTGGACTGAGGTTCTATGCCTTCAACCCTCTGGCTGGGGACCTGC
TGACTGGCAAGTACAAGTATAAGGACAAGGACAGGAAACAGCCCATGGGCCGCTTCTTTGGGACTCAATGGGCAGAGATC
TACAGGAATCGCTTCTGGAAGAAGCACCACTTCGATGGCATTGCCCTGGTAGAGAAGGCCCTGCAGGCCGCGTATGGCGC
CAGCGCCCCCAGCATGACCTCGGCTGCCCTCTGGTGGATGTACCACCACTCACAGCTGCAGGGTGCCCACGGGGACGCAG
TCATCCTGGGCATGTCCAGCTTGGAGCAGTTGGAGCAGAACTTGGCAGCGGCAGAGGAAGGGCCCCTGGAGCCAGATGTT
GTGGAGGCCTTTAATCAAGCCTGGCAATTGGTTGCTCACGAATGTCCCAACTACTTC

Alignment

ORF - retro_hsap_208 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.26 %
• Parental protein coverage: 78.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VKIDTKAIPLFGNSLKPDSLRFQLETSLKRLQCPRVDLFYLHMPDHSTPVEETLRACHQLHQEGKFVELG
          .KIDTKA.PLFGNSLKPDSLRFQLETSLK.LQCPRVDLFYL..PDHSTPVEETL.ACHQLHQEGKF..LG
Retrocopy LKIDTKANPLFGNSLKPDSLRFQLETSLKWLQCPRVDLFYLLRPDHSTPVEETLSACHQLHQEGKFLDLG

Parental  LSNYAAWEVAEICTLCKSNGWILPTVYQGMYNAITRQVETELFPCLRHFGLRFYAFNPLAGGLLTGKYKY
          LSNYA.WEVA.IC.LCKSNGW.LPTVYQGMYNA.T.QV.TELFPCLRH.GLRFYAFNPLAG.LLTGKYKY
Retrocopy LSNYATWEVAKICNLCKSNGWTLPTVYQGMYNATTQQVKTELFPCLRHSGLRFYAFNPLAGDLLTGKYKY

Parental  EDKNGKQPVGRFFGNTWAEMYRNRYWKEHHFEGIALVEKALQAAYGASAPSMTSATLRWMYHHSQLQGAH
          .DK..KQP.GRFFG..WAE.YRNR.WK.HHF.GIALVEKALQAAYGASAPSMTSA.L.WMYHHSQLQGAH
Retrocopy KDKDRKQPMGRFFGTQWAEIYRNRFWKKHHFDGIALVEKALQAAYGASAPSMTSAALWWMYHHSQLQGAH

Parental  GDAVILGMSSLEQLEQNLAAAEEGPLEPAVVDAFNQAWHLVTHECPNYF
          GDAVILGMSSLEQLEQNLAAAEEGPLEP.VV.AFNQAW.LV.HECPNYF
Retrocopy GDAVILGMSSLEQLEQNLAAAEEGPLEPDVVEAFNQAWQLVAHECPNYF

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	0.04 RPM	0.24 RPM
bodymap2_adrenal	0.18 RPM	0.61 RPM
bodymap2_brain	0.02 RPM	0.45 RPM
bodymap2_breast	0.00 RPM	0.25 RPM
bodymap2_colon	0.15 RPM	2.07 RPM
bodymap2_heart	0.04 RPM	0.06 RPM
bodymap2_kidney	0.00 RPM	12.55 RPM
bodymap2_liver	0.00 RPM	22.01 RPM
bodymap2_lung	0.04 RPM	0.21 RPM
bodymap2_lymph_node	0.00 RPM	0.16 RPM
bodymap2_ovary	0.06 RPM	0.50 RPM
bodymap2_prostate	0.00 RPM	0.19 RPM
bodymap2_skeletal_muscle	0.18 RPM	0.04 RPM
bodymap2_testis	0.04 RPM	0.49 RPM
bodymap2_thyroid	0.06 RPM	0.30 RPM
bodymap2_white_blood_cells	0.00 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_hsap_208 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CMI	POLR2A	1:113466195..113466692

EST

1 EST(s) were mapped to retro_hsap_208 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BF765305	113466129	113466408	98.6	274	4	269

TSS

No TSS is located nearby retro_hsap_208 retrocopy 5' end.

Lab

retro_hsap_208 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_208 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_431

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000162482	1 retrocopy	retro_hsap_208 ,
Macaca mulatta	ENSMMUG00000006891	1 retrocopy	retro_mmul_2629,
Nomascus leucogenys	ENSNLEG00000007852	1 retrocopy	retro_nleu_1857,
Pongo abelii	ENSPPYG00000001793	1 retrocopy	retro_pabe_431,
Pan troglodytes	ENSPTRG00000000265	1 retrocopy	retro_ptro_336,