RetrogeneDB ID: retro_sscr_35

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 6:77758761..77759508(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000003562
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: YWHAZ
• Ensembl ID: ENSSSCG00000006062
• Aliases: None
• Description: None

Sequence

>retro_sscr_35
ATGGAGAGAGCCAGTGTGATCCAGAAGGCCAAGTTGGCCGAGCAGGCTGAACGCTATGAGGACATGGCAGCCTTCATGAA
GAGCGCCGTGGAAAAGGGTGAGGAGCTGTCTTGCGAAGAGCGCAACCTGCTCTCAGTGGCCTACAAGAATGTGGTGGGTG
GTCAGCGGGCTGCGTGGAGGGTCCTGTCCAGTATTGAGCAGAAGAGCAATGAGGAAGGCTCGGAAGAGAAGGGCCCTGAG
GTGCGAGAATATCGGGAGAAGGTGGAGAAGGAGCTCCGGGGTGTGTGTGACACGGTGCTTGGCTTGCTGAACACCCATCT
CATCAAGGAGGCCGGTGACGCGGAGAGTCGGGTCTTCTACCTGAAAATGAAGGGTGACTACTACCGTTACCTGGCCGAGG
TGGCCACGGGGGACGACAAGAAGCGCATCATCGACTCAGCCCGCTCCGCCTACCAGGAGGCCATGGACATCAGCAAGAAA
GAGATGCCACCCACCAACCCCATCCGCCTGGGCCTGGCCCTGAACTTTTCTGTCTTCCACTATGAGATCGCCAACAGCCC
AGAGGAGGCCATCTCCCTGGCCAAGACCACCTTCGACGAGGCCATGGCTGACCTGCACACTCTCAGCGAGGACTCCTACA
AAGACAGCACCCTCATCATGCAGCTGCTGCGGGACAACCTGACGCTGTGGACCGCCGACAACGCCGGGGAAGAGGGGGGC
GAGGCGCCTGAGGAGCCCCAGAGCTGA

Alignment

ORF - retro_sscr_35 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.27 %
• Parental protein coverage: 95.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSVAYKNVVGARRSSWRVVSSIEQKT-
          M......QKAKLAEQAERY.DMAA.MKS..E.G.ELS.EERNLLSVAYKNVVG..R..WRV.SSIEQK..
Retrocopy MERASVIQKAKLAEQAERYEDMAAFMKSAVEKGEELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKSN

Parental  -EGAEKKQQMAREYREKIETELRDICNDVLSLLEKFLIPNASQAESKVFYLKMKGDYYRYLAEVAAGDDK
          .EG.E.K....REYREK.E.ELR..C..VL.LL...LI..A..AES.VFYLKMKGDYYRYLAEVA.GDDK
Retrocopy EEGSEEKGPEVREYREKVEKELRGVCDTVLGLLNTHLIKEAGDAESRVFYLKMKGDYYRYLAEVATGDDK

Parental  KGIVDQSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLSE
          K.I.D....AYQEA..ISKKEM.PT.PIRLGLALNFSVF.YEI.NSPE.A.SLAKT.FDEA.A.L.TLSE
Retrocopy KRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAISLAKTTFDEAMADLHTLSE

Parental  ESYKDSTLIMQLLRDNLTLWTSDTQGDE
          .SYKDSTLIMQLLRDNLTLWT.D..G.E
Retrocopy DSYKDSTLIMQLLRDNLTLWTADNAGEE

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
SRP014902_placenta	2313.24 RPM	174.94 RPM
SRP014902_testis	0.14 RPM	168.04 RPM
SRP018288_heart	0.08 RPM	99.64 RPM
SRP018288_kidney	0.20 RPM	118.31 RPM
SRP018288_liver	0.00 RPM	37.10 RPM
SRP018288_lung	2.75 RPM	176.57 RPM
SRP018856_adipose	0.97 RPM	262.30 RPM
SRP035408_brain	0.13 RPM	508.23 RPM
SRP035408_liver	0.06 RPM	68.31 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

9 EST(s) were mapped to retro_sscr_35 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AJ660998	77758708	77759082	100	374	0	374
BG835435	77758701	77759107	100	405	0	404
EW157942	77758909	77759205	100	296	0	296
EW440938	77758711	77759040	100	328	0	327
EW440954	77758802	77759101	100	299	0	299
EW443386	77758703	77759057	100	354	0	354
EW445586	77758788	77759043	100	255	0	255
EW651198	77759090	77759315	100	225	0	225
EW652725	77758930	77759085	98.1	155	0	154

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_35 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_35 has 10 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_8
Pan troglodytes	retro_ptro_3
Gorilla gorilla	retro_ggor_211
Pongo abelii	retro_pabe_103
Callithrix jacchus	retro_cjac_31
Mus musculus	retro_mmus_163
Oryctolagus cuniculus	retro_ocun_248
Bos taurus	retro_btau_86
Canis familiaris	retro_cfam_233
Equus caballus	retro_ecab_31

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Parental genes homology:

Parental genes homology involve 35 parental genes, and 134 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,
Choloepus hoffmanni	ENSCHOG00000002798	9 retrocopies	retro_chof_1572, retro_chof_1703, retro_chof_1890, retro_chof_2321, retro_chof_2346, retro_chof_2669, retro_chof_292, retro_chof_315, retro_chof_933,
Callithrix jacchus	ENSCJAG00000015844	5 retrocopies	retro_cjac_1769, retro_cjac_2164, retro_cjac_3000, retro_cjac_31, retro_cjac_881,
Cavia porcellus	ENSCPOG00000020285	5 retrocopies	retro_cpor_220, retro_cpor_323, retro_cpor_434, retro_cpor_592, retro_cpor_644,
Dasypus novemcinctus	ENSDNOG00000001672	10 retrocopies	retro_dnov_1007, retro_dnov_117, retro_dnov_1354, retro_dnov_1579, retro_dnov_1769, retro_dnov_1907, retro_dnov_1993, retro_dnov_2588, retro_dnov_892, retro_dnov_99,
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	ENSG00000164924	1 retrocopy	retro_hsap_549,
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,
Loxodonta africana	ENSLAFG00000004944	2 retrocopies	retro_lafr_1089, retro_lafr_112,
Myotis lucifugus	ENSMLUG00000017323	3 retrocopies	retro_mluc_1617, retro_mluc_1686, retro_mluc_296,
Macaca mulatta	ENSMMUG00000006489	7 retrocopies	retro_mmul_1859, retro_mmul_1883, retro_mmul_2136, retro_mmul_2247, retro_mmul_2422, retro_mmul_2503, retro_mmul_451,
Monodelphis domestica	ENSMODG00000006158	8 retrocopies	retro_mdom_1589, retro_mdom_1664, retro_mdom_1763, retro_mdom_1815, retro_mdom_1875, retro_mdom_1958, retro_mdom_255, retro_mdom_446,
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,
Nomascus leucogenys	ENSNLEG00000003220	7 retrocopies	retro_nleu_1368, retro_nleu_1426, retro_nleu_2186, retro_nleu_23, retro_nleu_449, retro_nleu_487, retro_nleu_722,
Oryctolagus cuniculus	ENSOCUG00000000734	2 retrocopies	retro_ocun_1091, retro_ocun_248,
Ochotona princeps	ENSOPRG00000000276	3 retrocopies	retro_opri_1218, retro_opri_218, retro_opri_967,
Procavia capensis	ENSPCAG00000010744	1 retrocopy	retro_pcap_170,
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 ,
Sus scrofa	ENSSSCG00000007381	1 retrocopy	retro_sscr_506,
Ictidomys tridecemlineatus	ENSSTOG00000023864	3 retrocopies	retro_itri_162, retro_itri_483, retro_itri_887,
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,
Tursiops truncatus	ENSTTRG00000015906	4 retrocopies	retro_ttru_15, retro_ttru_1540, retro_ttru_207, retro_ttru_455,
Vicugna pacos	ENSVPAG00000005865	1 retrocopy	retro_vpac_350,