RetrogeneDB ID: retro_hsap_549

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 10:23425852..23426587(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000229932
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: YWHAZ
• Ensembl ID: ENSG00000164924
• Aliases: YWHAZ, 14-3-3-zeta, HEL-S-3, HEL4, KCIP-1, YWHAD
• Description: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide [Source:HGNC Symbol;Acc:12855]

Sequence

>retro_hsap_549
ATGGATAAAAATGAGCTGGTTCAGAAGGCCAAACTGGCCGAGCAGGCTGAGCGATATGATGACATGGCAGCCTGCATGAA
GTCTGTAACTGAGCAAGGAGCTGAATTATCCAATGAGGAAAGGAATCTCCTCTCAGTTGCTTATAAAAATGTTGTAGGAG
CCCATAGGTCATCTTGGAGGGTCGTCTCAAGTATTGAACAAAAGACGGAGGGAGCTGAGAAAAAACAGCAGATGGCTCGC
GAATACAGAGAGAAAATTGAGACGGAGCTAAGAGATATCTGCAATGATGTACTGTCTCTTTTGGAAAAGTTCTTGATCCC
CAGTGCTTCACAAGCAGAGAGCAAAGTCTTCTATTTGAAAATGGAAGGAGATTACTACCGTTACTTGGCTGAGGTTGCCG
CTGGGGATGACAAGAAAGGGATTGTGGATCAGTCACAACAAGCGTACCAAGAAGCTTTTGAAATCAGCAAAAAGGAAATG
CAACCAACACATCCTATCAGACTGGGTCTGGCCCTTAACTTCTCTGTGTTCTATTATGAGATTCTGAACTCCCCAGAGAA
AGCCTGCTCTCTTGCAAAGACAGCTTTTGATGAAGCCATTGCTGAACTTGATACATTAAGTGAAGAGTCATACAAAGACA
GCACGCTAATAATGCAATTACTGAGGGACAACCTGACACTGTGGACATCAGATACCCAAGCAGACGAAGGTGAAGCAGGA
GAAGGAGTGGAAAAT

Alignment

ORF - retro_hsap_549 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSVAYKNVVGARRSSWRVVSSIEQKTE
          MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSVAYKNVVGA.RSSWRVVSSIEQKTE
Retrocopy MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSVAYKNVVGAHRSSWRVVSSIEQKTE

Parental  GAEKKQQMAREYREKIETELRDICNDVLSLLEKFLIPNASQAESKVFYLKMKGDYYRYLAEVAAGDDKKG
          GAEKKQQMAREYREKIETELRDICNDVLSLLEKFLIP.ASQAESKVFYLKM.GDYYRYLAEVAAGDDKKG
Retrocopy GAEKKQQMAREYREKIETELRDICNDVLSLLEKFLIPSASQAESKVFYLKMEGDYYRYLAEVAAGDDKKG

Parental  IVDQSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLSEES
          IVDQSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLSEES
Retrocopy IVDQSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLSEES

Parental  YKDSTLIMQLLRDNLTLWTSDTQGDEAEAGEGGEN
          YKDSTLIMQLLRDNLTLWTSDTQ.DE.EAGEG.EN
Retrocopy YKDSTLIMQLLRDNLTLWTSDTQADEGEAGEGVEN

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	0.97 RPM	660.15 RPM
bodymap2_adrenal	0.68 RPM	554.52 RPM
bodymap2_brain	0.84 RPM	969.27 RPM
bodymap2_breast	0.64 RPM	746.16 RPM
bodymap2_colon	0.48 RPM	524.64 RPM
bodymap2_heart	0.02 RPM	231.70 RPM
bodymap2_kidney	0.25 RPM	515.58 RPM
bodymap2_liver	0.00 RPM	134.37 RPM
bodymap2_lung	0.05 RPM	733.12 RPM
bodymap2_lymph_node	0.07 RPM	581.96 RPM
bodymap2_ovary	1.37 RPM	729.76 RPM
bodymap2_prostate	0.02 RPM	696.58 RPM
bodymap2_skeletal_muscle	0.02 RPM	163.76 RPM
bodymap2_testis	0.32 RPM	487.18 RPM
bodymap2_thyroid	0.85 RPM	443.49 RPM
bodymap2_white_blood_cells	0.35 RPM	1411.20 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_549 was not detected

EST

No EST(s) were mapped for retro_hsap_549 retrocopy.

TSS

No TSS is located nearby retro_hsap_549 retrocopy 5' end.

Lab

retro_hsap_549 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_549 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_412
Gorilla gorilla	retro_ggor_499
Pongo abelii	retro_pabe_89

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 80 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008694	2 retrocopies	retro_acar_25, retro_acar_44,
Ailuropoda melanoleuca	ENSAMEG00000000328	1 retrocopy	retro_amel_562,
Bos taurus	ENSBTAG00000000236	4 retrocopies	retro_btau_1482, retro_btau_635, retro_btau_68, retro_btau_910,
Canis familiaris	ENSCAFG00000000580	6 retrocopies	retro_cfam_1302, retro_cfam_1521, retro_cfam_158, retro_cfam_1840, retro_cfam_233, retro_cfam_465,
Callithrix jacchus	ENSCJAG00000015844	5 retrocopies	retro_cjac_1769, retro_cjac_2164, retro_cjac_3000, retro_cjac_31, retro_cjac_881,
Equus caballus	ENSECAG00000021882	3 retrocopies	retro_ecab_202, retro_ecab_31, retro_ecab_624,
Ficedula albicollis	ENSFALG00000005860	1 retrocopy	retro_falb_13,
Felis catus	ENSFCAG00000032017	4 retrocopies	retro_fcat_1563, retro_fcat_1631, retro_fcat_1697, retro_fcat_60,
Homo sapiens	ENSG00000108953	4 retrocopies	retro_hsap_2324, retro_hsap_3739, retro_hsap_3851, retro_hsap_4703,
Homo sapiens	ENSG00000134308	2 retrocopies	retro_hsap_3004, retro_hsap_8,
Homo sapiens	ENSG00000164924	1 retrocopy	retro_hsap_549 ,
Homo sapiens	ENSG00000166913	4 retrocopies	retro_hsap_4160, retro_hsap_4841, retro_hsap_622, retro_hsap_855,
Gallus gallus	ENSGALG00000010725	1 retrocopy	retro_ggal_3,
Gorilla gorilla	ENSGGOG00000022133	9 retrocopies	retro_ggor_1092, retro_ggor_1754, retro_ggor_211, retro_ggor_2379, retro_ggor_2997, retro_ggor_2998, retro_ggor_3020, retro_ggor_499, retro_ggor_544,
Mustela putorius furo	ENSMPUG00000015158	4 retrocopies	retro_mputfur_1000, retro_mputfur_239, retro_mputfur_7, retro_mputfur_864,
Mus musculus	ENSMUSG00000022285	3 retrocopies	retro_mmus_163, retro_mmus_2187, retro_mmus_744,
Oryctolagus cuniculus	ENSOCUG00000000734	2 retrocopies	retro_ocun_1091, retro_ocun_248,
Pongo abelii	ENSPPYG00000018791	7 retrocopies	retro_pabe_103, retro_pabe_1242, retro_pabe_2047, retro_pabe_3417, retro_pabe_3740, retro_pabe_556, retro_pabe_89,
Pelodiscus sinensis	ENSPSIG00000003703	1 retrocopy	retro_psin_13,
Pteropus vampyrus	ENSPVAG00000016641	1 retrocopy	retro_pvam_1101,
Sarcophilus harrisii	ENSSHAG00000012671	2 retrocopies	retro_shar_126, retro_shar_409,
Sus scrofa	ENSSSCG00000006062	2 retrocopies	retro_sscr_222, retro_sscr_35,
Taeniopygia guttata	ENSTGUG00000012078	1 retrocopy	retro_tgut_4,
Tarsius syrichta	ENSTSYG00000006150	10 retrocopies	retro_tsyr_1047, retro_tsyr_1075, retro_tsyr_1419, retro_tsyr_1941, retro_tsyr_2022, retro_tsyr_2066, retro_tsyr_2085, retro_tsyr_720, retro_tsyr_900, retro_tsyr_985,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.19 RPM
CEU_NA11843	0.09 RPM
CEU_NA11930	0.42 RPM
CEU_NA12004	0.08 RPM
CEU_NA12400	0.07 RPM
CEU_NA12751	0.10 RPM
CEU_NA12760	0.49 RPM
CEU_NA12827	0.57 RPM
CEU_NA12872	0.16 RPM
CEU_NA12873	0.22 RPM
FIN_HG00183	0.16 RPM
FIN_HG00277	0.26 RPM
FIN_HG00315	0.19 RPM
FIN_HG00321	0.15 RPM
FIN_HG00328	0.12 RPM
FIN_HG00338	0.13 RPM
FIN_HG00349	0.28 RPM
FIN_HG00375	0.05 RPM
FIN_HG00377	0.13 RPM
FIN_HG00378	0.36 RPM
GBR_HG00099	0.20 RPM
GBR_HG00111	0.09 RPM
GBR_HG00114	0.13 RPM
GBR_HG00119	0.07 RPM
GBR_HG00131	0.11 RPM
GBR_HG00133	0.17 RPM
GBR_HG00134	0.09 RPM
GBR_HG00137	0.08 RPM
GBR_HG00142	0.19 RPM
GBR_HG00143	0.19 RPM
TSI_NA20512	0.06 RPM
TSI_NA20513	0.22 RPM
TSI_NA20518	0.42 RPM
TSI_NA20532	0.10 RPM
TSI_NA20538	0.09 RPM
TSI_NA20756	0.15 RPM
TSI_NA20765	0.21 RPM
TSI_NA20771	0.23 RPM
TSI_NA20786	0.18 RPM
TSI_NA20798	0.09 RPM
YRI_NA18870	0.27 RPM
YRI_NA18907	0.17 RPM
YRI_NA18916	0.15 RPM
YRI_NA19093	0.31 RPM
YRI_NA19099	0.35 RPM
YRI_NA19114	0.16 RPM
YRI_NA19118	0.08 RPM
YRI_NA19213	0.14 RPM
YRI_NA19214	0.15 RPM
YRI_NA19223	0.20 RPM

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Indel association:

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