RetrogeneDB ID: retro_hsap_1972

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 19:18141437..18142836(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000268032
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CS
• Ensembl ID: ENSG00000062485
• Aliases: None
• Description: citrate synthase [Source:HGNC Symbol;Acc:2422]

Sequence

>retro_hsap_1972
ATGGCTTTACTTACTGCGGCCGCCCGGCTCTTGGGAACCAAGAATGCATCTTGTCTTGTTCTTGCAGCCCAGCATGCCAG
TGCTTCCTCCATGAATTTGAAAGACATATTGGCTGACCTCATACCTAAGGAGCAGGCCAGAATTAAGACCTTCAGGCAGC
AACATGGCAAGAAGGTGGTGGGCCAAATCACTGTGGACATGATGTATGGTGGCATGAGAGGCATGAAGGGATTGGTCTAT
GAAACATCAGTTCTTGATCCTGATGAGGGCATCCGTTTCTGAGGCTTTAGTATCCCTGAATGCCAGAAACTGCTACCCAA
GGCTAAGGGTGGGGAAGAACCCCTGCCTGAGGGCTTATTTTGGCTGCTGGTAACTGGATGTATCCCAACAGAGGAACAGG
TATCTTGGCTCTCAAAAGAGTGGGCAAAGAGGGCAGCTCTGCCTTCCCATGTGGTCACCATGCTGGACAACTTTCCCACC
AATCTACACCCCATGTCTCAGCTCAGTGCAGCTGTTACAGCCCTCAACAGTGAAAGTAACTTTGCCCAAGCATATGCACG
GGGTATCAGCCGAACCCAAGTACTGGGAGTTGATTTATGAAGACTCTGTGGATCTAATCACAAAGCTACCTTGTGTCGCA
GCAAAGATCTACCGAAATCTCTATGGAGAAGGCAGTGGTATTGGGGCCATTGACTCTAACCTGGACTGGTCTCACAGTTT
CACCAACATGTTAGGCTATACTGATCATCAGTTCCCTGAGCTCATGCACCTGTACCTCACTATCCACAGTGACCATGAGG
GCGGCAATGTAAGTGCCCATACCAGCCACTTGGTGGGCAGTGGCCTTTCAGACCCTTACCTGTCCTTTGCAGCAGCCATG
AACGGGCTGGCAGGGCCTCTCCATGGACTGGCAAATCAGGAAGTGCTTGTCTGGCTAACACAGCTGCAGAAGGAAGTTGG
CAAAGATGTGTCAGATGAGAAGTTATGAGACTACATCTGGAACACACTCAACTCAGGACGGGCTGTTCCAGGCTATGGCC
ATGCAGTACTAAGGAAGACTGATCCACGATATACCTGTCAGCGAGAGTTTGCTCTGAAACACCTGCCTAATGACCCCATG
TTTAAGTTGGTTGCTCAGCTATGCAAGATTGTGCCCAATGTCCTCTTAGAGCAGGGTAAGGCCAAGAATCCTTGGCCCAA
TGTAGATGCTCACAGTGGGGTGCTGCTCCAGTATTATGGCATGATGGAGATGAATTACTACACAGTCCTGTTTGGGGTGT
CACGAGCATTGGGTGTACTGGCACAGCTCATCTGGAGCCGAGCCTTAGGCTTCCCTCTAGAAAGGCCCAAGTCCATGAGC
ACAGAGGGTCTGATGAAGTTTGTGGACTCTAAGTCAGGG

Alignment

ORF - retro_hsap_1972 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.72 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALLTAAARLLGTKNASCLVLAARHASASSTNLKDILADLIPKEQARIKTFRQQHGKTVVGQITVDMMYG
          MALLTAAARLLGTKNASCLVLAA.HASASS.NLKDILADLIPKEQARIKTFRQQHGK.VVGQITVDMMYG
Retrocopy MALLTAAARLLGTKNASCLVLAAQHASASSMNLKDILADLIPKEQARIKTFRQQHGKKVVGQITVDMMYG

Parental  GMRGMKGLVYETSVLDPDEGIRFRGFSIPECQKLLPKAKGGEEPLPEGLFWLLVTGHIPTEEQVSWLSKE
          GMRGMKGLVYETSVLDPDEGIRF.GFSIPECQKLLPKAKGGEEPLPEGLFWLLVTG.IPTEEQVSWLSKE
Retrocopy GMRGMKGLVYETSVLDPDEGIRF*GFSIPECQKLLPKAKGGEEPLPEGLFWLLVTGCIPTEEQVSWLSKE

Parental  WAKRAALPSHVVTMLDNFPTNLHPMSQLSAAVTALNSESNFARAYAQGISRT-KYWELIYEDSMDLIAKL
          WAKRAALPSHVVTMLDNFPTNLHPMSQLSAAVTALNSESNFA.AYA.GISRT.KYWELIYEDS.DLI.KL
Retrocopy WAKRAALPSHVVTMLDNFPTNLHPMSQLSAAVTALNSESNFAQAYARGISRT>KYWELIYEDSVDLITKL

Parental  PCVAAKIYRNLYREGSGIGAIDSNLDWSHNFTNMLGYTDHQFTELTRLYLTIHSDHEGGNVSAHTSHLVG
          PCVAAKIYRNLY.EGSGIGAIDSNLDWSH.FTNMLGYTDHQF.EL..LYLTIHSDHEGGNVSAHTSHLVG
Retrocopy PCVAAKIYRNLYGEGSGIGAIDSNLDWSHSFTNMLGYTDHQFPELMHLYLTIHSDHEGGNVSAHTSHLVG

Parental  SALSDPYLSFAAAMNGLAGPLHGLANQEVLVWLTQLQKEVGKDVSDEKLRDYIWNTLNSGRVVPGYGHAV
          S.LSDPYLSFAAAMNGLAGPLHGLANQEVLVWLTQLQKEVGKDVSDEKL.DYIWNTLNSGR.VPGYGHAV
Retrocopy SGLSDPYLSFAAAMNGLAGPLHGLANQEVLVWLTQLQKEVGKDVSDEKL*DYIWNTLNSGRAVPGYGHAV

Parental  LRKTDPRYTCQREFALKHLPNDPMFKLVAQLYKIVPNVLLEQGKAKNPWPNVDAHSGVLLQYYGMTEMNY
          LRKTDPRYTCQREFALKHLPNDPMFKLVAQL.KIVPNVLLEQGKAKNPWPNVDAHSGVLLQYYGM.EMNY
Retrocopy LRKTDPRYTCQREFALKHLPNDPMFKLVAQLCKIVPNVLLEQGKAKNPWPNVDAHSGVLLQYYGMMEMNY

Parental  YTVLFGVSRALGVLAQLIWSRALGFPLERPKSMSTEGLMKFVDSKSG
          YTVLFGVSRALGVLAQLIWSRALGFPLERPKSMSTEGLMKFVDSKSG
Retrocopy YTVLFGVSRALGVLAQLIWSRALGFPLERPKSMSTEGLMKFVDSKSG

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	1.09 RPM	180.81 RPM
bodymap2_adrenal	0.14 RPM	123.00 RPM
bodymap2_brain	1.03 RPM	110.78 RPM
bodymap2_breast	0.29 RPM	292.34 RPM
bodymap2_colon	0.17 RPM	128.08 RPM
bodymap2_heart	0.24 RPM	403.19 RPM
bodymap2_kidney	0.02 RPM	174.15 RPM
bodymap2_liver	0.04 RPM	50.49 RPM
bodymap2_lung	0.25 RPM	116.03 RPM
bodymap2_lymph_node	0.05 RPM	119.02 RPM
bodymap2_ovary	0.27 RPM	124.88 RPM
bodymap2_prostate	0.07 RPM	141.23 RPM
bodymap2_skeletal_muscle	0.91 RPM	302.85 RPM
bodymap2_testis	0.23 RPM	80.33 RPM
bodymap2_thyroid	0.73 RPM	134.13 RPM
bodymap2_white_blood_cells	0.33 RPM	149.90 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1972 was not detected

EST

No EST(s) were mapped for retro_hsap_1972 retrocopy.

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_71369	665 libraries	567 libraries	536 libraries	48 libraries	13 libraries

The graphical summary, for retro_hsap_1972 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_1972 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1972 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004371	1 retrocopy	retro_btau_386,
Canis familiaris	ENSCAFG00000000115	1 retrocopy	retro_cfam_765,
Choloepus hoffmanni	ENSCHOG00000000397	1 retrocopy	retro_chof_1803,
Callithrix jacchus	ENSCJAG00000011275	1 retrocopy	retro_cjac_2031,
Dasypus novemcinctus	ENSDNOG00000010907	2 retrocopies	retro_dnov_205, retro_dnov_468,
Echinops telfairi	ENSETEG00000012035	1 retrocopy	retro_etel_584,
Homo sapiens	ENSG00000062485	2 retrocopies	retro_hsap_1972 , retro_hsap_3621,
Gorilla gorilla	ENSGGOG00000009096	2 retrocopies	retro_ggor_1432, retro_ggor_2445,
Macropus eugenii	ENSMEUG00000005657	2 retrocopies	retro_meug_1078, retro_meug_1304,
Microcebus murinus	ENSMICG00000017659	2 retrocopies	retro_mmur_1322, retro_mmur_394,
Macaca mulatta	ENSMMUG00000002483	2 retrocopies	retro_mmul_1502, retro_mmul_1840,
Mus musculus	ENSMUSG00000005683	1 retrocopy	retro_mmus_258,
Nomascus leucogenys	ENSNLEG00000017514	2 retrocopies	retro_nleu_1201, retro_nleu_809,
Oryctolagus cuniculus	ENSOCUG00000007216	1 retrocopy	retro_ocun_1183,
Pongo abelii	ENSPPYG00000004654	1 retrocopy	retro_pabe_2972,
Rattus norvegicus	ENSRNOG00000023520	1 retrocopy	retro_rnor_2518,
Sorex araneus	ENSSARG00000010093	2 retrocopies	retro_sara_360, retro_sara_628,
Sus scrofa	ENSSSCG00000021091	1 retrocopy	retro_sscr_321,
Sus scrofa	ENSSSCG00000022858	1 retrocopy	retro_sscr_322,
Tupaia belangeri	ENSTBEG00000006425	1 retrocopy	retro_tbel_4652,
Tarsius syrichta	ENSTSYG00000004483	1 retrocopy	retro_tsyr_1659,