RetrogeneDB ID: retro_hsap_97

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:21874602..21875721(+)
• Located in intron of: ENSG00000012174

Retrocopy information

• Ensembl ID: ENSG00000230797
• Aliases: YY2, ZNF631
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: YY1
• Ensembl ID: ENSG00000100811
• Aliases: None
• Description: YY1 transcription factor [Source:HGNC Symbol;Acc:12856]

Sequence

>retro_hsap_97
ATGGCCTCCAACGAAGATTTCTCCATCACACAAGACCTGGAGATCCCGGCAGATATTGTGGAGCTCCACGACATCAATGT
GGAGCCCCTTCCTATGGAGGACATTCCGACGGAAAGCGTCCAGTACGAGGATGTGGATGGCAATTGGATCTACGGTGGCC
ACAACCATCCGCCATTGATGGTGTTGCAGCCGCTCTTCACGAACACGGGCTATGGCGACCACGACCAGGAAATGCTTATG
TTGCAGACACAAGAGGAAGTGGTGGGCTATTGCGACTCAGACAACCAGCTAGGCAACGACTTGGAGGACCAGTTGGCCCT
CCCGGATAGCATTGAAGACGAGCACTTCCAGATGACCCTGGCCTCTCTGTCGGCCTCGGCGGCATCAACATCAACATCAA
CCCAGAGCCGCAGCAAAAAGCCCAGCAAAAAGCCCAGCGGCAAGAGTGCCACCAGCACTGAGGCCAACCCGGCAGGCAGC
AGCTCCAGCCTGGGCACGAGGAAGTGGGAGCAGAAGCAAATGCAGGTCAAAACGCTGGAGGGTGAGTTTTCCGTGACTAT
GTGGTCCCCTAACGATAACAATGACCAAGGGGCAGTGGGTGAAGGCCAGGCTGAAAACCCACCTGATTATTCCGAGTACT
TGAAAGGGAAGAAACTTCCTCCTGGGGGGTTACCAGGCATTGATCTCTCAGATCCTAAACAGCTGGCAGAATTTACTAAA
GTGAAGCCCAAAAGGTCCAAAGGAGAACCTCCCAAAACAGTCCCTTGCTCTTATAGCGGCTGCGAAAAGATGTTCCGGGA
TTACGCCGCCATGAGAAAACATCTCCACATCCACGGGCCCAGAGTCCACGTATGTGCAGAATGTGGCAAAGCTTTTCTTG
AGAGCTCAAAGCTGAGACGACACCAGCTGGTCCACACCGGCGAGAAGCCCTTTCAGTGCACATTCGAAGGCTGCGGGAAA
CGCTTTTCCCTTGATTTCAATTTGCGCACACACTTGCGCATCCACACCGGCGATAAGCCCTTCGTGTGCCCCTTCGATGT
TTGCAACAGGAAGTTCGCTCAGTCAACCAACCTGAAAACCCACATATTAACGCATGTGAAGACCAAAAACAACCCGTGA

Alignment

ORF - retro_hsap_97 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.71 %
• Parental protein coverage: 81.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HHHPPMIALQPLVTDDPTQVHHHQEVILVQTREEVVGGDDSDGLRAEDGFEDQILIPVPAPAGGDDDYIE
          H.HPP...LQPL.T.......H.QE....QT.EEVVG..DSD.....D..EDQ.......P....D....
Retrocopy HNHPPLMVLQPLFT-NTGYGDHDQEMLMLQTQEEVVGYCDSDNQLGND-LEDQLAL----PDSIEDEHFQ

Parental  QTLVTVAAAGKSGGGGSSSSGGGRVKKGGGKKSGKKSYLSGGAGAAGGGGADPGNKKWEQKQVQIKTLEG
          .TL....A...S.....S.S...R.KK...K.SGK.S..S..A..AG......G..KWEQKQ.Q.KTLEG
Retrocopy MTLASLSASAAS----TSTSTQSRSKKPSKKPSGK-SATSTEANPAGSSSS-LGTRKWEQKQMQVKTLEG

Parental  EFSVTMWSSDEKKDIDHETVVEEQIIGENSPPDYSEYMTGKKLPPGGIPGIDLSDPKQLAEFARMKPRKI
          EFSVTMWS.......D...V.E.Q......PPDYSEY..GKKLPPGG.PGIDLSDPKQLAEF...KP...
Retrocopy EFSVTMWSPNDNN--DQGAVGEGQA---ENPPDYSEYLKGKKLPPGGLPGIDLSDPKQLAEFTKVKPKRS

Parental  KEDDAPRTIACPHKGCTKMFRDNSAMRKHLHTHGPRVHVCAECGKAFVESSKLKRHQLVHTGEKPFQCTF
          K....P.T..C...GC.KMFRD..AMRKHLH.HGPRVHVCAECGKAF.ESSKL.RHQLVHTGEKPFQCTF
Retrocopy K-GEPPKTVPCSYSGCEKMFRDYAAMRKHLHIHGPRVHVCAECGKAFLESSKLRRHQLVHTGEKPFQCTF

Parental  EGCGKRFSLDFNLRTHVRIHTGDRPYVCPFDGCNKKFAQSTNLKSHILTHAKAKNN
          EGCGKRFSLDFNLRTH.RIHTGD.P.VCPFD.CN.KFAQSTNLK.HILTH.K.KNN
Retrocopy EGCGKRFSLDFNLRTHLRIHTGDKPFVCPFDVCNRKFAQSTNLKTHILTHVKTKNN

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	94.06 RPM
bodymap2_adrenal	0.33 RPM	114.34 RPM
bodymap2_brain	0.26 RPM	90.36 RPM
bodymap2_breast	0.51 RPM	109.69 RPM
bodymap2_colon	0.35 RPM	145.12 RPM
bodymap2_heart	0.17 RPM	76.08 RPM
bodymap2_kidney	0.50 RPM	104.39 RPM
bodymap2_liver	0.76 RPM	67.34 RPM
bodymap2_lung	0.37 RPM	124.17 RPM
bodymap2_lymph_node	0.58 RPM	162.40 RPM
bodymap2_ovary	0.79 RPM	130.12 RPM
bodymap2_prostate	0.40 RPM	130.21 RPM
bodymap2_skeletal_muscle	0.40 RPM	109.93 RPM
bodymap2_testis	4.92 RPM	123.98 RPM
bodymap2_thyroid	1.05 RPM	123.76 RPM
bodymap2_white_blood_cells	0.32 RPM	224.15 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_97 was not detected

EST

2 EST(s) were mapped to retro_hsap_97 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BX955529	21874848	21875178	100	330	0	330
DA961884	21874578	21875132	100	554	0	554

TSS

No TSS is located nearby retro_hsap_97 retrocopy 5' end.

Lab

retro_hsap_97 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_97 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011146	1 retrocopy	retro_amel_2,
Bos taurus	ENSBTAG00000020819	1 retrocopy	retro_btau_91,
Callithrix jacchus	ENSCJAG00000016853	2 retrocopies	retro_cjac_1931, retro_cjac_4045,
Cavia porcellus	ENSCPOG00000020809	2 retrocopies	retro_cpor_1220, retro_cpor_1522,
Equus caballus	ENSECAG00000005805	1 retrocopy	retro_ecab_97,
Homo sapiens	ENSG00000100811	2 retrocopies	retro_hsap_106, retro_hsap_97 ,
Gorilla gorilla	ENSGGOG00000026332	2 retrocopies	retro_ggor_190, retro_ggor_2,
Mustela putorius furo	ENSMPUG00000002931	1 retrocopy	retro_mputfur_867,
Mus musculus	ENSMUSG00000021264	1 retrocopy	retro_mmus_190,
Nomascus leucogenys	ENSNLEG00000000999	3 retrocopies	retro_nleu_1092, retro_nleu_116, retro_nleu_2225,
Oryctolagus cuniculus	ENSOCUG00000026938	1 retrocopy	retro_ocun_1871,
Otolemur garnettii	ENSOGAG00000006955	4 retrocopies	retro_ogar_1231, retro_ogar_1804, retro_ogar_1857, retro_ogar_289,
Pongo abelii	ENSPPYG00000025949	3 retrocopies	retro_pabe_145, retro_pabe_3616, retro_pabe_534,
Pan troglodytes	ENSPTRG00000006717	3 retrocopies	retro_ptro_3093, retro_ptro_45, retro_ptro_494,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.94 RPM
CEU_NA11843	0.74 RPM
CEU_NA11930	1.04 RPM
CEU_NA12004	1.29 RPM
CEU_NA12400	0.49 RPM
CEU_NA12751	1.55 RPM
CEU_NA12760	0.72 RPM
CEU_NA12827	1.37 RPM
CEU_NA12872	1.20 RPM
CEU_NA12873	0.70 RPM
FIN_HG00183	1.35 RPM
FIN_HG00277	1.40 RPM
FIN_HG00315	1.27 RPM
FIN_HG00321	1.09 RPM
FIN_HG00328	0.57 RPM
FIN_HG00338	0.55 RPM
FIN_HG00349	1.11 RPM
FIN_HG00375	0.81 RPM
FIN_HG00377	0.86 RPM
FIN_HG00378	1.27 RPM
GBR_HG00099	1.10 RPM
GBR_HG00111	0.92 RPM
GBR_HG00114	1.24 RPM
GBR_HG00119	1.20 RPM
GBR_HG00131	0.89 RPM
GBR_HG00133	0.84 RPM
GBR_HG00134	0.94 RPM
GBR_HG00137	1.02 RPM
GBR_HG00142	0.97 RPM
GBR_HG00143	1.31 RPM
TSI_NA20512	0.73 RPM
TSI_NA20513	1.48 RPM
TSI_NA20518	1.47 RPM
TSI_NA20532	1.53 RPM
TSI_NA20538	0.69 RPM
TSI_NA20756	1.40 RPM
TSI_NA20765	1.57 RPM
TSI_NA20771	1.50 RPM
TSI_NA20786	0.97 RPM
TSI_NA20798	0.31 RPM
YRI_NA18870	1.15 RPM
YRI_NA18907	1.04 RPM
YRI_NA18916	1.18 RPM
YRI_NA19093	1.12 RPM
YRI_NA19099	0.88 RPM
YRI_NA19114	0.58 RPM
YRI_NA19118	1.16 RPM
YRI_NA19213	0.93 RPM
YRI_NA19214	1.80 RPM
YRI_NA19223	1.95 RPM

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Indel association:

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