RetrogeneDB ID: retro_dord_486

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_22603:16405..16961(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ccng1
• Ensembl ID: ENSDORG00000014293
• Aliases: None
• Description: cyclin G1 [Source:MGI Symbol;Acc:MGI:102890]

Sequence

>retro_dord_486
GTACAGCCCAAGCACCTTGGGTGTGTTGGCCTGAGCTGCTTTTACTTGGCTGTAAAGTCAATAGAAGAGGAAAGGAATGT
CCCTTTGGCAATTGACTTGAGCTGAATAAGTCAGTATAGATGTACAGTTTCAGACTTTGATGAGAATGGGAAAGACTGTC
TTGGAGAAGGAGTGTTGGACAGTTCAAGCTACAAGGGCCTTTCAGTTTCTACAACTCTCTTCTTCCTGCATTCAGGAGAT
CTTGCTATCTGAAAGAAAAAATACATTTGATTTGGAAAGACTAGAAGCTCAACTTAAGGCATGTCACTGCAGAATCGTAT
TTTCTAAAGCAAAGCCTTTGGTGTTGGCACTATTCATCATGTGCCTGGAGATCCAGGCACAGAAGATTATAGAATTAACA
GAGGGTGGTGAATGCCTTCCGAAACATTCCAAGATAAGTGGTCGGGATTTGATCTTCTGGTAAGAGCTTGTATCCAAGTG
TTTAACTGAATATTCATCAAACAAGTGCTCCAAACCAAACATTCAGAAGTTGAAGTAGATTGTTTCCGGGTAGACG

Alignment

ORF - retro_dord_486 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.65 %
• Parental protein coverage: 89.37 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VQPKHLGCVGLSCFYLAVKSIEEERNVPSATDLIRISQYRFTVSD-LMRMEKIVLEKVCWKVRATTAFQF
          VQPKHLGCVGLSCFYLAVKSIEEERNVP.A.DL..ISQYR.TVSD.LMRM.K.VLEK.CW.V.AT.AFQF
Retrocopy VQPKHLGCVGLSCFYLAVKSIEEERNVPLAIDLS*ISQYRCTVSD>LMRMGKTVLEKECWTVQATRAFQF

Parental  LQLYSSLIQENLPPERRNSLNFERLEAQLKACHCRILFSKAKPSVLALSIVALEIQAQKALELTEGVECL
          LQL.SS.IQE.L..ER.N....ERLEAQLKACHCRI.FSKAKP.VLAL.I..LEIQAQK..ELTEG.ECL
Retrocopy LQLSSSCIQEILLSERKNTFDLERLEAQLKACHCRIVFSKAKPLVLALFIMCLEIQAQKIIELTEGGECL

Parental  QKHSKISARDLIFWQELVSKCLTEYSSNKCSKPNVQKLKWIVSGRT
          .KHSKIS.RDLIFW.ELVSKCLTEYSSNKCSKPN.QKLK.IVSG.T
Retrocopy PKHSKISGRDLIFW*ELVSKCLTEYSSNKCSKPNIQKLK*IVSG*T

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq

Dipodomys ordii was not studied using ChIP-Seq data.

EST

Dipodomys ordii was not studied using EST data.

TSS

Dipodomys ordii was not studied using FANTOM5 data.

Lab

retro_dord_486 was not experimentally validated.

Homology

Retrocopy orthology:

Dipodomys ordii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 18 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,
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,
Oryctolagus cuniculus	ENSOCUG00000002129	3 retrocopies	retro_ocun_1287, retro_ocun_512, retro_ocun_615,
Otolemur garnettii	ENSOGAG00000007639	1 retrocopy	retro_ogar_2452,
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,