RetrogeneDB ID: retro_hsap_42

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 15:59499139..59500285(+)
• Located in intron of: ENSG00000157483

Retrocopy information

• Ensembl ID: ENSG00000171989
• Aliases: LDHAL6B, LDH6B, LDHAL6, LDHL
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: LDHAL6A
• Ensembl ID: ENSG00000166800
• Aliases: LDHAL6A, LDH6A
• Description: lactate dehydrogenase A-like 6A [Source:HGNC Symbol;Acc:28335]

Sequence

>retro_hsap_42
ATGAGTTGGACTGTGCCTGTTGTGCGGGCCAGCCAGAGAGTGAGCTCGGTGGGAGCGAATTTCCTATGCCTGGGGATGGC
CCTGTGTCCGCGTCAAGCAACGCGCATCCCGCTCAACGGCACCTGGCTCTTCACCCCCGTGAGCAAGATGGCGACTGTGA
AGAGTGAGCTTATTGAGCGTTTCACTTCCGAGAAGCCCGTTCATCACAGTAAGGTCTCCATCATAGGAACTGGATCGGTG
GGCATGGCCTGCGCTATCAGCATCTTATTAAAAGGCTTGAGTGATGAACTTGCCCTTGTGGATCTTGATGAAGACAAACT
GAAGGGTGAGACGATGGATCTTCAACATGGCAGCCCTTTCACGAAAATGCCAAATATTGTTTGTAGCAAAGATTACTTTG
TCACAGCAAACTCCAACCTAGTGATTATCACAGCAGGTGCACGCCAAGAAAAGGGAGAAACGCGCCTTAATTTAGTCCAG
CGAAATGTGGCCATCTTCAAGTTAATGATTTCCAGTATTGTCCAGTACAGCCCCCACTGCAAACTGATTATTGTTTCCAA
TCCAGTGGATATCTTAACTTATGTAGCTTGGAAGTTGAGTGCATTTCCCAAAAACCGTATTATTGGAAGCGGCTGTAATC
TGGATACTGCTCGTTTTCGTTTCTTGATTGGACAAAAGCTTGGTATCCATTCTGAAAGCTGCCATGGATGGATCCTCGGA
GAGCATGGAGACTCAAGTGTTCCTGTGTGGAGTGGAGTGAACATAGCTGGTGTCCCTTTGAAGGATCTGAACTCTGATAT
AGGAACTGATAAAGATCCTGAGCAATGGAAAAATGTCCACAAAGAAGTGACTGCAACTGCCTATGAGATTATTAAAATGA
AAGGTTATACTTCTTGGGCCATTGGCCTATCTGTGGCCGATTTAACAGAAAGTATTTTGAAGAATCTTAGGAGAATACAT
CCAGTTTCCACCATAATTAAGGGCCTCTATGGAATAGATGAAGAAGTATTCCTCAGTATTCCTTGTATCCTGGGAGAGAA
CGGTATTACCAACCTTATAAAGATAAAGCTGACCCCTGAAGAAGAGGCCCATCTGAAAAAAAGTGCAAAAACACTCTGGG
AAATTCAGAATAAGCTTAAGCTTTAA

Alignment

ORF - retro_hsap_42 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.23 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATIKSELIKNFAEEEAIHHNKISIVGTGSVGVACAISILLKGLSDELVLVDVDEGKLKGETMDLQHGSP
          MAT.KSELI..F..E...HH.K.SI.GTGSVG.ACAISILLKGLSDEL.LVD.DE.KLKGETMDLQHGSP
Retrocopy MATVKSELIERFTSEKPVHHSKVSIIGTGSVGMACAISILLKGLSDELALVDLDEDKLKGETMDLQHGSP

Parental  FMKMPNIVSSKDYLVTANSNLVIITAGARQKKGETRLDLVQRNVSIFKLMIPNITQYSPHCKLLIVTNPV
          F.KMPNIV.SKDY.VTANSNLVIITAGARQ.KGETRL.LVQRNV.IFKLMI..I.QYSPHCKL.IV.NPV
Retrocopy FTKMPNIVCSKDYFVTANSNLVIITAGARQEKGETRLNLVQRNVAIFKLMISSIVQYSPHCKLIIVSNPV

Parental  DILTYVAWKLSGFPKNRVIGSGCNLDSARFRYFIGQRLGIHSESCHGLILGEHGDSSVPVWSGVNIAGVP
          DILTYVAWKLS.FPKNR.IGSGCNLD.ARFR..IGQ.LGIHSESCHG.ILGEHGDSSVPVWSGVNIAGVP
Retrocopy DILTYVAWKLSAFPKNRIIGSGCNLDTARFRFLIGQKLGIHSESCHGWILGEHGDSSVPVWSGVNIAGVP

Parental  LKDLNPDIGTDKDPEQWENVHKKVISSGYEMVKMKGYTSWGISLSVADLTESILKNLRRVHPVSTLSKGL
          LKDLN.DIGTDKDPEQW.NVHK.V....YE..KMKGYTSW.I.LSVADLTESILKNLRR.HPVST..KGL
Retrocopy LKDLNSDIGTDKDPEQWKNVHKEVTATAYEIIKMKGYTSWAIGLSVADLTESILKNLRRIHPVSTIIKGL

Parental  YGINEDIFLSVPCILGENGITDLIKVKLTLEEEACLQKSAETLWEIQKELKL
          YGI.E..FLS.PCILGENGIT.LIK.KLT.EEEA.L.KSA.TLWEIQ..LKL
Retrocopy YGIDEEVFLSIPCILGENGITNLIKIKLTPEEEAHLKKSAKTLWEIQNKLKL

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	0.58 RPM	0.24 RPM
bodymap2_adrenal	0.41 RPM	0.84 RPM
bodymap2_brain	0.14 RPM	0.59 RPM
bodymap2_breast	0.12 RPM	0.16 RPM
bodymap2_colon	0.33 RPM	0.04 RPM
bodymap2_heart	0.02 RPM	0.06 RPM
bodymap2_kidney	0.25 RPM	0.97 RPM
bodymap2_liver	0.00 RPM	0.00 RPM
bodymap2_lung	0.00 RPM	0.00 RPM
bodymap2_lymph_node	0.00 RPM	0.27 RPM
bodymap2_ovary	0.12 RPM	0.71 RPM
bodymap2_prostate	0.33 RPM	0.00 RPM
bodymap2_skeletal_muscle	0.11 RPM	0.00 RPM
bodymap2_testis	16.40 RPM	7.33 RPM
bodymap2_thyroid	0.15 RPM	0.79 RPM
bodymap2_white_blood_cells	0.00 RPM	0.45 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_42 was not detected

EST

30 EST(s) were mapped to retro_hsap_42 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AW953921	59499106	59499693	98.5	574	8	560
BG718803	59499064	59499666	100	602	0	602
BP368794	59499092	59499645	97.3	535	15	520
BU561631	59499073	59499702	97.8	624	4	614
CV024257	59499139	59499776	99.1	632	3	628
CV375046	59499138	59499593	98.1	446	7	435
DB021204	59499107	59499589	98.4	477	3	472
DB021438	59499067	59499617	99	547	3	543
DB022472	59499061	59499618	99.5	557	0	556
DB024248	59499061	59499621	99.5	557	3	554
DB025209	59499061	59499559	99.4	494	3	491
DB027291	59499064	59499649	99.5	582	3	579
DB032702	59499032	59499570	99.9	537	1	536
DB035729	59499103	59499685	100	581	0	581
DB041618	59499049	59499613	99.5	561	3	558
DB042270	59499064	59499619	98.8	551	4	546
DB046642	59499064	59499603	99.5	536	3	533
DB052936	59499064	59499627	99.2	558	5	553
DB055157	59499068	59499622	99	551	3	547
DB441948	59499071	59499492	97.4	415	4	406
DB442183	59499064	59499497	98	427	4	418
DB446851	59499071	59499512	99.4	438	3	435
DB452514	59499073	59499559	99.2	482	4	478
HY008337	59499069	59499602	99.3	529	4	525
HY010322	59499072	59499570	99.6	496	2	494
HY010617	59499107	59499668	99.7	559	2	557
HY015264	59499064	59499593	99.3	525	4	521
HY026718	59499064	59499551	100	486	0	486
HY047922	59499107	59499563	99.8	455	1	454
HY243389	59499107	59499527	100	420	0	420

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_45076	1824 libraries	2 libraries	1 library	0 libraries	2 libraries
TSS #2	TSS_45077	1822 libraries	3 libraries	1 library	0 libraries	3 libraries
TSS #3	TSS_45078	1823 libraries	3 libraries	2 libraries	1 library	0 libraries

The graphical summary, for retro_hsap_42 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_42 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_42 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_62
Pongo abelii	retro_pabe_203
Macaca mulatta	retro_mmul_261
Callithrix jacchus	retro_cjac_164

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007067	2 retrocopies	retro_cjac_164, retro_cjac_2180,
Homo sapiens	ENSG00000111716	1 retrocopy	retro_hsap_4863,
Homo sapiens	ENSG00000134333	5 retrocopies	retro_hsap_2097, retro_hsap_2285, retro_hsap_3021, retro_hsap_323, retro_hsap_4231,
Homo sapiens	ENSG00000166800	2 retrocopies	retro_hsap_42 , retro_hsap_905,
Macaca mulatta	ENSMMUG00000014614	2 retrocopies	retro_mmul_1111, retro_mmul_261,
Nomascus leucogenys	ENSNLEG00000017780	2 retrocopies	retro_nleu_29, retro_nleu_378,
Otolemur garnettii	ENSOGAG00000009261	1 retrocopy	retro_ogar_2662,
Pongo abelii	ENSPPYG00000003435	2 retrocopies	retro_pabe_203, retro_pabe_779,
Pan troglodytes	ENSPTRG00000003423	1 retrocopy	retro_ptro_62,
Tarsius syrichta	ENSTSYG00000008062	4 retrocopies	retro_tsyr_1811, retro_tsyr_2064, retro_tsyr_2071, retro_tsyr_731,