RetrogeneDB ID: retro_mmus_2187

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:92689424..92690160(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000091421
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ywhaz
• Ensembl ID: ENSMUSG00000022285
• Aliases: Ywhaz, 1110013I11Rik, 14-3-3zeta, AI596267, AL022924, AU020854
• Description: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide [Source:MGI Symbol;Acc:MGI:109484]

Sequence

>retro_mmus_2187
ATGGATAAAAATGAGCTGGTGCAGAAGGCCAAGCTGGCCGAGCAGGCAGAGCGATATGATGACATGGCAGCCTGCATGAA
GTCTGTCACTGAGCAGGGAGCTGAGCTGTCGAATGAGGAGAGAAACCTTCTCTCTGTTGCTTATAAAAAACGTTGTAGGA
GCCCGTAGGTCATCGTGGAGGGTCGTCTCAAGTATTGAGCAGAAGACGGAAGGTGCTGAGAAAAAGCAGCAGATGGCTCG
AGAATACAGAGAGAAGATCGAGACGGAGCTGCGTGACATCTGCAACGATGTACTGTCTCTTTTGGAAAAGTTCTTGATCC
CCAATGCTTCGCAACCAGAAAGCAAAGTCTTCTATTTGAAAATGAAGGGTGACTACTACCGTTACTTGGCCGAGGTTGCT
GCTGGTGATGACAAGAAAGGAATTGTGGACCAGTCACAGCAAGCATACCAAGAAGCATTTGAAATCAGCAAAAAGGAGAT
GCAGCCGACACACCCCATCAGACTGGGTCTGGCCCTCAACTTCTCTGTGTTCTATTACGAGATCCTGAACTCCCCAGAGA
AAGCCTGCTCTCTTGCAAAAACAGCTTTCGATGAAGCCATTGCTGAACTTGATACATTAAGTGAAGAGTCGTACAAAGAC
AGCACGCTAATAATGCAGTTACTGAGAGACAACTTAACATTGTGGACATCGGATACCCAAGGAGATGAAGCAGAAGCAGG
AGAAGGAGGGGAAAAT

Alignment

ORF - retro_mmus_2187 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.59 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSVAY-KNVVGARRSSWRVVSSIEQKT
          MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSVAY.KNVVGARRSSWRVVSSIEQKT
Retrocopy MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSVAY>KNVVGARRSSWRVVSSIEQKT

Parental  EGAEKKQQMAREYREKIETELRDICNDVLSLLEKFLIPNASQPESKVFYLKMKGDYYRYLAEVAAGDDKK
          EGAEKKQQMAREYREKIETELRDICNDVLSLLEKFLIPNASQPESKVFYLKMKGDYYRYLAEVAAGDDKK
Retrocopy EGAEKKQQMAREYREKIETELRDICNDVLSLLEKFLIPNASQPESKVFYLKMKGDYYRYLAEVAAGDDKK

Parental  GIVDQSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLSEE
          GIVDQSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLSEE
Retrocopy GIVDQSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLSEE

Parental  SYKDSTLIMQLLRDNLTLWTSDTQGDEAEAGEGGEN
          SYKDSTLIMQLLRDNLTLWTSDTQGDEAEAGEGGEN
Retrocopy SYKDSTLIMQLLRDNLTLWTSDTQGDEAEAGEGGEN

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
SRP007412_brain	1.59 RPM	458.26 RPM
SRP007412_cerebellum	0.52 RPM	217.63 RPM
SRP007412_heart	0.25 RPM	51.05 RPM
SRP007412_kidney	1.06 RPM	179.21 RPM
SRP007412_liver	0.11 RPM	47.57 RPM
SRP007412_testis	0.32 RPM	65.77 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2187 was not detected

EST

1 EST(s) were mapped to retro_mmus_2187 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BY229018	92689458	92689848	99.8	386	1	384

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_97459	167 libraries	250 libraries	197 libraries	258 libraries	200 libraries
TSS #2	TSS_97460	361 libraries	55 libraries	3 libraries	51 libraries	602 libraries
TSS #3	TSS_97461	91 libraries	121 libraries	708 libraries	133 libraries	19 libraries

The graphical summary, for retro_mmus_2187 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 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_mmus_2187 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2187 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 35 parental genes, and 143 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,
Mus musculus	ENSMUSG00000076432	10 retrocopies	retro_mmus_1076, retro_mmus_1378, retro_mmus_1926, retro_mmus_2250, retro_mmus_2299, retro_mmus_2471, retro_mmus_2689, retro_mmus_3250, retro_mmus_3308, retro_mmus_406,
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,
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,