RetrogeneDB ID: retro_mmus_3530

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:145833316..145834131(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000080915
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Phb
• Ensembl ID: ENSMUSG00000038845
• Aliases: Phb, Bap32
• Description: prohibitin [Source:MGI Symbol;Acc:MGI:97572]

Sequence

>retro_mmus_3530
ATGGCTGCCAAAGCTTTCAAGTCCATGGGAAAGCTCAGTCTGGTGTTAGCAGTTGCAGTAGGTGTGGTGAACTCTGCTTT
ATGTAATGTAGGTGTTGGACACAGAACTGTTTTCTCTGACAAATTCCATGGAGTACAGGACATTGTGGTAAGGAAAGGGA
TTCACTTTCTCAACCCTTGGGTAGAGAAACCAATTATCTTTGACTGCTGCTTTTGACCATGAAATGTGCCCATTGTCACC
GGGAGCAGACTTGCAGAATGTCAACATCACATTGATCATCCTCTTCTGGCTGATTGCCAGCTAGTTTCCTCATTCCTATA
CAAGCATTGGTGAGGACTATGATGAGCGAGTGTTGCCATCTATCACCACAGAGATCTTCAAGTTGGTGGTGGCTCAAATC
GATGCTGGAGAGTTAGTTACCCAGCGAGAACTGGTCTCCAGGCAGGTGAGCGATGACCTCACAGAGCAAGCAGCAACATT
TGGGCTTATCCTGGATGACATATACCTGACACATCTGACCTTCAGGAAGGAGTTCACAGAGACAATAAAAGCCAAACAGA
TGGCTCAGCAGGAAGCAAGAGAGAGCCAGATTTATGGTGGAAAAGGCTGAGCAGCAGCAGAAGGCAGCCATCATCTCTGC
TGAGAGTGACTCCAAGGAAGATGAGCTGATTGTCAATTCGCTGGCCACAGCAGATGCTGGCCTGATTGAGCTGCAAAAGC
TGGAAGCTGCTGAGGACATTGCATACCAGCACTGCCACTCTCCGAACATCATCTACCTGCCAGCAGGGCAGTCTGTGCTC
CTCCAGCTTCTCCAG

Alignment

ORF - retro_mmus_3530 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAKVFESIGKFGLALAVAGGVVNSALYNVDAGHRAVIFDRFRGVQDIVVGEGTHFLIPWVQKPIIFDCR
          MAAK.F.S.GK..L.LAVA.GVVNSAL.NV..GHR.V..D.F.GVQDIVV..G.HFL.PWV.KPIIFDC.
Retrocopy MAAKAFKSMGKLSLVLAVAVGVVNSALCNVGVGHRTVFSDKFHGVQDIVVRKGIHFLNPWVEKPIIFDCC

Parental  SRPRNV-PVITGSKDLQNVNITLRILFRPVASQLPRIYTSIGEDYDERVLPSITTEILKSVVARFDAGEL
          ..P.NV.P...G..DLQNVNITL.ILF...AS..P..YTSIGEDYDERVLPSITTEI.K.VVA..DAGEL
Retrocopy F*P*NV>PLSPGA-DLQNVNITLIILFWLIAS*FPHSYTSIGEDYDERVLPSITTEIFKLVVAQIDAGEL

Parental  ITQRELVSRQVSDDLTERAATFGLILDDVSLTHLTFGKEFTEAVEAKQVAQQEA-ERARFVVEKAEQQKK
          .TQRELVSRQVSDDLTE.AATFGLILDD..LTHLTF.KEFTE...AKQ.AQQEA.ERARF.VEKAEQQ.K
Retrocopy VTQRELVSRQVSDDLTEQAATFGLILDDIYLTHLTFRKEFTETIKAKQMAQQEA>ERARFMVEKAEQQQK

Parental  AAIISAEGDSKAAELIANSLATAGDGLIELRKLEAAEDIAYQLSRSRNITYLPAGQSVLLQLPQ
          AAIISAE.DSK..ELI.NSLATA..GLIEL.KLEAAEDIAYQ...S.NI.YLPAGQSVLLQL.Q
Retrocopy AAIISAESDSKEDELIVNSLATADAGLIELQKLEAAEDIAYQHCHSPNIIYLPAGQSVLLQLLQ

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	0.00 RPM	17.43 RPM
SRP007412_cerebellum	0.00 RPM	19.89 RPM
SRP007412_heart	0.00 RPM	63.66 RPM
SRP007412_kidney	0.00 RPM	43.68 RPM
SRP007412_liver	0.00 RPM	25.48 RPM
SRP007412_testis	0.00 RPM	2.88 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3530 was not detected

EST

No EST(s) were mapped for retro_mmus_3530 retrocopy.

TSS

No TSS is located nearby retro_mmus_3530 retrocopy 5' end.

Lab

retro_mmus_3530 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3530 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_2855

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 87 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004797	1 retrocopy	retro_acar_49,
Canis familiaris	ENSCAFG00000016926	1 retrocopy	retro_cfam_202,
Choloepus hoffmanni	ENSCHOG00000007588	2 retrocopies	retro_chof_1159, retro_chof_2193,
Callithrix jacchus	ENSCJAG00000007174	22 retrocopies	retro_cjac_1048, retro_cjac_1403, retro_cjac_1683, retro_cjac_1761, retro_cjac_1820, retro_cjac_2261, retro_cjac_2389, retro_cjac_2390, retro_cjac_2391, retro_cjac_2445, retro_cjac_2523, retro_cjac_2659, retro_cjac_2663, retro_cjac_2909, retro_cjac_4205, retro_cjac_570, retro_cjac_635, retro_cjac_662, retro_cjac_872, retro_cjac_937, retro_cjac_966, retro_cjac_980,
Erinaceus europaeus	ENSEEUG00000006481	3 retrocopies	retro_eeur_219, retro_eeur_285, retro_eeur_369,
Gorilla gorilla	ENSGGOG00000028002	12 retrocopies	retro_ggor_124, retro_ggor_1722, retro_ggor_1876, retro_ggor_238, retro_ggor_2387, retro_ggor_246, retro_ggor_2607, retro_ggor_3053, retro_ggor_476, retro_ggor_643, retro_ggor_741, retro_ggor_870,
Macropus eugenii	ENSMEUG00000005122	1 retrocopy	retro_meug_708,
Myotis lucifugus	ENSMLUG00000008203	2 retrocopies	retro_mluc_116, retro_mluc_2190,
Macaca mulatta	ENSMMUG00000000156	13 retrocopies	retro_mmul_1096, retro_mmul_1119, retro_mmul_1165, retro_mmul_1425, retro_mmul_151, retro_mmul_1565, retro_mmul_2148, retro_mmul_2420, retro_mmul_426, retro_mmul_521, retro_mmul_834, retro_mmul_866, retro_mmul_933,
Monodelphis domestica	ENSMODG00000012210	1 retrocopy	retro_mdom_812,
Mus musculus	ENSMUSG00000038845	8 retrocopies	retro_mmus_1089, retro_mmus_1321, retro_mmus_3522, retro_mmus_3530 , retro_mmus_3535, retro_mmus_3649, retro_mmus_3657, retro_mmus_822,
Otolemur garnettii	ENSOGAG00000027015	1 retrocopy	retro_ogar_968,
Procavia capensis	ENSPCAG00000008851	1 retrocopy	retro_pcap_74,
Rattus norvegicus	ENSRNOG00000046799	18 retrocopies	retro_rnor_1058, retro_rnor_1416, retro_rnor_1540, retro_rnor_1542, retro_rnor_2398, retro_rnor_2399, retro_rnor_2610, retro_rnor_2653, retro_rnor_2815, retro_rnor_2826, retro_rnor_2848, retro_rnor_2855, retro_rnor_2909, retro_rnor_292, retro_rnor_2948, retro_rnor_2949, retro_rnor_543, retro_rnor_898,
Tursiops truncatus	ENSTTRG00000010836	1 retrocopy	retro_ttru_639,