RetrogeneDB ID: retro_mmus_1534

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:89632887..89633415(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Ccng1
• Ensembl ID: ENSMUSG00000020326
• Aliases: Ccng1, AI314029
• Description: cyclin G1 [Source:MGI Symbol;Acc:MGI:102890]

Sequence

>retro_mmus_1534
AGCTCCTTCTGTCTGGCTGTAAAGTTAGTAAATGAAAAGAGGTCAGTTCCCCTGTCACCTGACTTGATCTGGCTAAGTCA
GTATGGATTTTGGGTTTCAAACCTGGTGAGAATGGAAAGAATTGTTTTAACGAAGGTGTGTTGGAAAGTCGAAGCCACTA
CTGCTGTTCACCATCTGCAGCTCTGCTACTTGCTCATTCAAGGAACTTGCCATTTAGAGGCAGAAATAGATTTACCTTTG
AAAGGGCAGGAACATCTCAACTATGGCAGGTCACTGCAGGATCATATGCCTATGTTCTAATGTAAAGCGTTCTGTGTTGG
CATAGACTGCCATTGCTTAGGAGAGCCAAGCACCCATGTGGGCAGAATGAAGGAAGGAACAGTGTCACCAGGAATATTCC
CAGATAAATGGCTGAGATTTGACCTTTGGGCAAGAGCTTGTATCCAAGCGTTTGATTGAATATTAATCAAGCACATGTTC
TAAACTAATGCTCAGAAGTTGAAATGACTCATTTCTGTGTACACTGCC

Alignment

ORF - retro_mmus_1534 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.51 %
• Parental protein coverage: 59.52 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SCFYLAVKATEEERNVPLATDLIRISQYRFTVSDLMRMEKIVLEKVCWKVKATTAFQFLQLYYSLVHDTL
          S.F.LAVK...E.R.VPL..DLI..SQY.F.VS.L.RME.IVL.KVCWKV.ATTA...LQL.Y.L...T.
Retrocopy SSFCLAVKLVNEKRSVPLSPDLIWLSQYGFWVSNLVRMERIVLTKVCWKVEATTAVHHLQLCYLLIQGTC

Parental  PFERRNDLNFERLE-AQLKACHCRIIF--SKAKPSVLALSILALEIQALKYVELTEGVECIQKHSKISGR
          ..E...DL.....E.....A.HCRII...S..K.SVLA....A.E.QA....E......C.Q..S.I.G.
Retrocopy HLEAEIDLPLKGQE>ISTMAGHCRIICLCSNVKRSVLA*TAIA*ESQAPMWAE*RKE-QCHQEYSQING*

Parental  DLTFWQELVSKCLTEYSSNKCSK-PNGQKLKWIVSGRTA
          DLTF.QELVSK.L.EY.S..CSK..N.QKLK...S..TA
Retrocopy DLTFGQELVSKRLIEY*SSTCSK<TNAQKLK*LISVYTA

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	62.82 RPM
SRP007412_cerebellum	0.00 RPM	32.31 RPM
SRP007412_heart	0.00 RPM	585.37 RPM
SRP007412_kidney	0.00 RPM	149.24 RPM
SRP007412_liver	0.00 RPM	22.88 RPM
SRP007412_testis	0.00 RPM	5.03 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1534 was not detected

EST

No EST(s) were mapped for retro_mmus_1534 retrocopy.

TSS

No TSS is located nearby retro_mmus_1534 retrocopy 5' end.

Lab

retro_mmus_1534 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1534 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006607	2 retrocopies	retro_btau_1064, retro_btau_763,
Canis familiaris	ENSCAFG00000017207	1 retrocopy	retro_cfam_1657,
Callithrix jacchus	ENSCJAG00000015341	1 retrocopy	retro_cjac_2319,
Cavia porcellus	ENSCPOG00000000880	1 retrocopy	retro_cpor_771,
Dasypus novemcinctus	ENSDNOG00000015166	1 retrocopy	retro_dnov_1275,
Dipodomys ordii	ENSDORG00000014293	1 retrocopy	retro_dord_486,
Equus caballus	ENSECAG00000018880	1 retrocopy	retro_ecab_152,
Felis catus	ENSFCAG00000027366	1 retrocopy	retro_fcat_763,
Myotis lucifugus	ENSMLUG00000001667	1 retrocopy	retro_mluc_1341,
Monodelphis domestica	ENSMODG00000007651	1 retrocopy	retro_mdom_1018,
Mus musculus	ENSMUSG00000020326	1 retrocopy	retro_mmus_1534 ,
Mus musculus	ENSMUSG00000063015	2 retrocopies	retro_mmus_1211, retro_mmus_2730,
Oryctolagus cuniculus	ENSOCUG00000002129	3 retrocopies	retro_ocun_1287, retro_ocun_512, retro_ocun_615,
Otolemur garnettii	ENSOGAG00000007639	1 retrocopy	retro_ogar_2452,
Pongo abelii	ENSPPYG00000016016	1 retrocopy	retro_pabe_3373,
Pteropus vampyrus	ENSPVAG00000017902	1 retrocopy	retro_pvam_1027,
Sarcophilus harrisii	ENSSHAG00000007465	2 retrocopies	retro_shar_328, retro_shar_490,
Vicugna pacos	ENSVPAG00000008340	1 retrocopy	retro_vpac_351,