RetrogeneDB ID: retro_hsap_674

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 10:52389286..52391008(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000231588
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SHQ1
• Ensembl ID: ENSG00000144736
• Aliases: SHQ1, Shq1p
• Description: SHQ1, H/ACA ribonucleoprotein assembly factor [Source:HGNC Symbol;Acc:25543]

Sequence

>retro_hsap_674
ATGCTGACCCCGGCGTTCAGCCTCAGCCAGGAGCCGGATTTCCTGACCATCGCCATCCGCGTGCCCTATGCCCCGGCCTC
CGAGTTCAACGTCTACTTCGAGGGGTCGGCCTAGACTACTATGCCAAGCCGTACTTTCTCAGATTAACCCCTCCTGGAAG
AATTGTAGAATATGGATACGGAAGCGAGCAAGGGTCCTATGATGCAGATAAAGGAATTTTTACCACTCGCCTGCCCAGAG
AAACCCCTGGCCAGCATTTTGAGGGGCTGAACATGTGTTGCTCTTCTGGCACCAGGAAAATCCGGGACAGCAAAACCACT
TGTGGAAGCAATAGGTGATTCTGAAATTCCTGAGGAAGTAGTTGACGATGAAGAGTTTGATTGGGAAATTGAGCAGACAC
CCTATGAAGAGGTAACAGAAAGTGCTTTGAATCCTCATGCCACTATGGGTTTGGAAACTTACGATCAGGAGTGTTTCAGC
AGTTACAGGATGAATTGAGTGATGTTATTAAGGATCCAGATTTCATCCCTGCAGCAGAACGAAAACAAAAGCACCTGGCC
GCCGAGCTGGCCAAGTTTGATCCTGATCATTATCTAGCTGACTTTTTTGAAGATGAGGCAGTTGAACAGATTTTGAAGTA
TAATCCTTGGTGGACTGACAAATATTAAAAAATGACGGCCTTTTTGGAAAAGAGTCAGAAGCAAGAAAATCATGCTGCAT
TAGTGTCTTTTTCTGAAGAAGAGAAATATCAGCTACAAGAATTTGTCAATAAATCTTATCTGCTAGACAACAGAGCCTGT
CGTCAAGTGTACTACAGTTCGATTGATATCCTTCTGGCATATTGCTAAGAAACCCGTGTCACTGAAGGAGACAAGAACGT
TGAATCTGCATGGAATATCACGAAACTTGAGTCCAATACTATGCTGGTTTGAGACTTGGACTAATGTTCATGATATCATG
GTGTCTTTTGGAAGAAGGGTATTGTGTTACCTGCTCTATCGCCATTTCAAACTGGCGATGAAGGCCTACGGGGAGACTAT
AAAGATACTGCAATTAAGTAAAAGTGCAGTTTTAAAGTGTCTCCTGGATATTCACAAAATTTTTCAGGAAAACGACCCAG
CATACATACTGAATGATCTCTACATCTCATACTACTGTGTGTGGACTCAGAAAGTCAAATCCAAAACGTTGGCAGCTCTT
GCAGAAGCCTTAAAGGAAGTCTCCCTTACAAAGGCCCAGTTGGGGTTAGAACTGGAAGAACTAGAAGCAGCAGCACTTCT
TGTCCAGGAGGAAGAATCTGCATTACAAGCAGCCCATTCAGTTTCTGGGCAGCAGAAACTTTGCTGCAGCTCTGAGGCAG
GTGATTCAGAGGACTCAGACAGCACTGTGTCATCTGGAAACAAAGACTCAGACTCACATTCAGAACAAGATGAACTCAAA
GATAGTCCATCTGAGACAGTTCTTTGCAAGGTCCCCTTCTTGAAGAAAGCAGTGCCCTTCTGATTGTTGATGGTGGAGTA
TGCAGAAACACAGCCATCCAGGAGTCTGATGCCAGTCAGGGAAAGCCACTTGCCTCTTCCCAGCCTCTTGGAGTGTCTGG
GCCTCTGATAGAGGAGCTTGGGGGAACAACTGAAGACCACCGTTCAGGTTTTTGAACCCGAGGGCACCACTGCTGTAGAC
CACATCAACATGCAGGAGAGAGATGGCTGTCAGACACCAAAT

Alignment

ORF - retro_hsap_674 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.27 %
• Parental protein coverage: 99.83 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MLTPAFDLSQDPDFLTIAIRVPYARVSEFDVYFEGS-DFKFYAKPYFLRLTLPGRIVEN--GSEQGSYDA
          MLTPAF.LSQ.PDFLTIAIRVPYA..SEF.VYFEGS.....YAKPYFLRLT.PGRIVE...GSEQGSYDA
Retrocopy MLTPAFSLSQEPDFLTIAIRVPYAPASEFNVYFEGS<GLDYYAKPYFLRLTPPGRIVEYGYGSEQGSYDA

Parental  DKGIFTIRLPKETPGQHFEGLNMLTALLAPRKSR-TAKPLVEEIGASEIPEEVVDDEEFDWEIEQTPCEE
          DKGIFT.RLP.ETPGQHFEGLNM.......RK.R.TAKPLVE.IG.SEIPEEVVDDEEFDWEIEQTP.EE
Retrocopy DKGIFTTRLPRETPGQHFEGLNMCCS-SGTRKIR>TAKPLVEAIGDSEIPEEVVDDEEFDWEIEQTPYEE

Parental  VSESALNP-QCHYGFGNLRSGVLQRLQDELSDVIDIKDPDFTPAAERRQKRLAAELAKFDPDHYLADFFE
          V.ESALNP..CHYGFGNLRSGV.Q.LQDELSDV..IKDPDF.PAAER.QK.LAAELAKFDPDHYLADFFE
Retrocopy VTESALNP<SCHYGFGNLRSGVFQQLQDELSDV--IKDPDFIPAAERKQKHLAAELAKFDPDHYLADFFE

Parental  DEAIEQILKYNPWWTDKYSKMMAFLEKSQEQENHATLVSFSEEEKYQLRKFVNKSYLLDKRACRQVCYSL
          DEA.EQILKYNPWWTDKY.KM.AFLEKSQ.QENHA.LVSFSEEEKYQL..FVNKSYLLD.RACRQV.YS.
Retrocopy DEAVEQILKYNPWWTDKY*KMTAFLEKSQKQENHAALVSFSEEEKYQLQEFVNKSYLLDNRACRQVYYSS

Parental  IDILLAYCYETRVTEGEKNVESAWNI-RKLSPTLCWFETWTNVHDIMVSFGRRVLCYPLYRHFKLVMKAY
          IDILLAYC.ETRVTEG.KNVESAWNI.R.LSP.LCWFETWTNVHDIMVSFGRRVLCY.LYRHFKL.MKAY
Retrocopy IDILLAYC*ETRVTEGDKNVESAWNI>RNLSPILCWFETWTNVHDIMVSFGRRVLCYLLYRHFKLAMKAY

Parental  RDTIKILQLGKSAVLKCLLDIHKIFQENDPAYILNDLYISDYCVWIQKVKSKKLAALAEALKEVSLTKAQ
          ..TIKILQL.KSAVLKCLLDIHKIFQENDPAYILNDLYIS.YCVW.QKVKSK.LAALAEALKEVSLTKAQ
Retrocopy GETIKILQLSKSAVLKCLLDIHKIFQENDPAYILNDLYISYYCVWTQKVKSKTLAALAEALKEVSLTKAQ

Parental  LGLELEELEAAALLVQEEETALKAAHSVSGQQTLCSSSEASDSEDSDSSVSSGNEDSGSDSEQDELKDSP
          LGLELEELEAAALLVQEEE.AL.AAHSVSGQQ.LC.SSEA.DSEDSDS.VSSGN.DS.S.SEQDELKDSP
Retrocopy LGLELEELEAAALLVQEEESALQAAHSVSGQQKLCCSSEAGDSEDSDSTVSSGNKDSDSHSEQDELKDSP

Parental  SETVSSLQGPF-LEESSAFLIVDGGVRRNTAIQESDASQGKPLASSWPLGVSGPLIEE-LGEQLKTTVQV
          SETV.....PF.LEESSA.LIVDGGV.RNTAIQESDASQGKPLASS.PLGVSGPLIEE.LGEQLKTTVQV
Retrocopy SETV-LCKVPF<LEESSALLIVDGGVCRNTAIQESDASQGKPLASSQPLGVSGPLIEE>LGEQLKTTVQV

Parental  SEPKGTTAVNRSNIQERDGCQTPN
          .EP.GTTAV...N.QERDGCQTPN
Retrocopy FEPEGTTAVDHINMQERDGCQTPN

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	2.21 RPM	10.79 RPM
bodymap2_adrenal	4.42 RPM	18.22 RPM
bodymap2_brain	0.66 RPM	6.73 RPM
bodymap2_breast	0.99 RPM	15.19 RPM
bodymap2_colon	0.19 RPM	12.03 RPM
bodymap2_heart	0.74 RPM	13.18 RPM
bodymap2_kidney	1.10 RPM	20.20 RPM
bodymap2_liver	0.47 RPM	9.25 RPM
bodymap2_lung	0.21 RPM	8.53 RPM
bodymap2_lymph_node	0.00 RPM	14.00 RPM
bodymap2_ovary	1.25 RPM	29.47 RPM
bodymap2_prostate	0.59 RPM	14.96 RPM
bodymap2_skeletal_muscle	0.51 RPM	17.26 RPM
bodymap2_testis	1.40 RPM	32.73 RPM
bodymap2_thyroid	2.60 RPM	23.90 RPM
bodymap2_white_blood_cells	3.17 RPM	24.63 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_674 was not detected

EST

No EST(s) were mapped for retro_hsap_674 retrocopy.

TSS

No TSS is located nearby retro_hsap_674 retrocopy 5' end.

Lab

retro_hsap_674 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_674 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_486
Gorilla gorilla	retro_ggor_581

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015131	1 retrocopy	retro_cjac_1045,
Homo sapiens	ENSG00000144736	1 retrocopy	retro_hsap_674 ,
Gorilla gorilla	ENSGGOG00000034818	1 retrocopy	retro_ggor_581,
Nomascus leucogenys	ENSNLEG00000002731	1 retrocopy	retro_nleu_463,
Pongo abelii	ENSPPYG00000013717	1 retrocopy	retro_pabe_546,
Pan troglodytes	ENSPTRG00000015106	1 retrocopy	retro_ptro_486,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	1.52 RPM
CEU_NA11843	0.88 RPM
CEU_NA11930	0.98 RPM
CEU_NA12004	1.10 RPM
CEU_NA12400	0.91 RPM
CEU_NA12751	2.43 RPM
CEU_NA12760	1.03 RPM
CEU_NA12827	0.80 RPM
CEU_NA12872	1.82 RPM
CEU_NA12873	1.12 RPM
FIN_HG00183	1.70 RPM
FIN_HG00277	1.55 RPM
FIN_HG00315	1.19 RPM
FIN_HG00321	1.45 RPM
FIN_HG00328	1.04 RPM
FIN_HG00338	1.11 RPM
FIN_HG00349	1.11 RPM
FIN_HG00375	1.30 RPM
FIN_HG00377	0.98 RPM
FIN_HG00378	1.38 RPM
GBR_HG00099	1.89 RPM
GBR_HG00111	1.31 RPM
GBR_HG00114	1.47 RPM
GBR_HG00119	2.11 RPM
GBR_HG00131	1.84 RPM
GBR_HG00133	1.35 RPM
GBR_HG00134	1.53 RPM
GBR_HG00137	0.71 RPM
GBR_HG00142	1.61 RPM
GBR_HG00143	0.83 RPM
TSI_NA20512	0.90 RPM
TSI_NA20513	2.37 RPM
TSI_NA20518	1.47 RPM
TSI_NA20532	1.19 RPM
TSI_NA20538	1.47 RPM
TSI_NA20756	0.81 RPM
TSI_NA20765	1.74 RPM
TSI_NA20771	1.19 RPM
TSI_NA20786	1.26 RPM
TSI_NA20798	1.50 RPM
YRI_NA18870	1.73 RPM
YRI_NA18907	2.15 RPM
YRI_NA18916	1.20 RPM
YRI_NA19093	1.72 RPM
YRI_NA19099	2.29 RPM
YRI_NA19114	0.81 RPM
YRI_NA19118	1.18 RPM
YRI_NA19213	1.34 RPM
YRI_NA19214	2.02 RPM
YRI_NA19223	2.31 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).