RetrogeneDB ID: retro_dord_501

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_24086:14525..15416(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cdk16
• Ensembl ID: ENSDORG00000002798
• Aliases: None
• Description: cyclin-dependent kinase 16 [Source:MGI Symbol;Acc:MGI:97516]

Sequence

>retro_dord_501
ATGGAAGACTATATCAAAATAGAAAAAATTGGAGAAGGTACTTATGGAGTTGTGTATAAGGGTAGACACAAAACAACAGG
CCAAATAGTAGCTATGAAAAAAATCAGACTGGAAAGTGAAGAGGAAGGGGTTCCTAGTACTGCCATTCGGGAAATTTCTC
TATTAAAAGAACTTCGTCATCCAAACATTGTCAGTCTTCAAGATGTGCTTATGCAGGATTCCAGGTTATATCTCATCTTT
GAATTCCTTTCCATGGATCTCAAGAAATACTTAGATTCTATCCCACCTGGTCAATTCATGGATTCTTCACTTGTTAAGAG
TTATTTGTACCAAATCCTTCAGGGGATTGTGTTTTGTCACTCTAGAAGGGTTCTTCACAGAGATTTAAAACCTCAAAATC
TATTGATTGATGATAAAGGAACTATCAAGCTGGCTGACTTTGGCCTTGCCAGAGCTTTTGGAATCCCTATTAGGGTATAT
ACACATGAGGTAGTGACACTTTGGTATAGATCTCCAGAAGTATTGCTGGGGTCAGCCCGTTACTCTACTCCAGTGGACAT
TTGGAGTATAGGCACCATATTTGCAGAGCTGGCAACTAAGAAGCCTCTTTTCCATGGGGATTCAGAAATCGATCAGCTCT
TCAGGATTTTCAGAGCCTTAGGTACTCCTAATAATGAAGTGTGGCCAGAAGTGGAATCTCTACAGGACTATAAGAATGCA
TTTCCCAAGTGGAAACCAGGAAGCCTTGCTTCCCATGTCAAAAATTTGGATGAAAATGGCTTGGATTTGCTCTCGAAAAT
GTTAGTCTATGATCCAGCCAAACGTATTTCTGGCAAAATGGCACTGAATCATCCATATTTTGATGATCTGGACAATCAAA
TTAAGAAGATG

Alignment

ORF - retro_dord_501 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.01 %
• Parental protein coverage: 59.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LETYIKLDKLGEGTYATVYKGKSKLTDNLVALKEIRLE-HEEGAPCTAIREVSLLKDLKHANIVTLHDII
          .E.YIK..K.GEGTY..VYKG..K.T...VA.K.IRLE..EEG.P.TAIRE.SLLK.L.H.NIV.L.D..
Retrocopy MEDYIKIEKIGEGTYGVVYKGRHKTTGQIVAMKKIRLESEEEGVPSTAIREISLLKELRHPNIVSLQDVL

Parental  HTEKSLTLVFEYLDKDLKQYLDDC--GNIINMHNVKLFLFQLLRGLAYCHRQKVLHRDLKPQNLLINERG
          .....L.L.FE.L..DLK.YLD....G.......VK..L.Q.L.G...CH...VLHRDLKPQNLLI...G
Retrocopy MQDSRLYLIFEFLSMDLKKYLDSIPPGQFMDSSLVKSYLYQILQGIVFCHSRRVLHRDLKPQNLLIDDKG

Parental  ELKLADFGLARAKSIPTKTYSNEVVTLWYRPPDILLGSTDYSTQIDMWGVGCIFYEMATGRPLFPGSTVE
          ..KLADFGLARA..IP...Y..EVVTLWYR.P..LLGS..YST..D.W..G.IF.E.AT..PLF.G....
Retrocopy TIKLADFGLARAFGIPIRVYTHEVVTLWYRSPEVLLGSARYSTPVDIWSIGTIFAELATKKPLFHGDSEI

Parental  EQLHFIFRILGTPTEETWPGIMSNEEFKTYNYPKYRAEALLSHAPRLDSDGADLLTKLLQFEGRNRISAE
          .QL..IFR.LGTP..E.WP...S....K....PK.....L.SH...LD..G.DLL.K.L......RIS..
Retrocopy DQLFRIFRALGTPNNEVWPEVESLQDYKN-AFPKWKPGSLASHVKNLDENGLDLLSKMLVYDPAKRISGK

Parental  DAMKHPFFFSLGERIHKL
          .A..HP.F..L...I.K.
Retrocopy MALNHPYFDDLDNQIKKM

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_501 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012261	1 retrocopy	retro_cjac_961,
Dipodomys ordii	ENSDORG00000002798	1 retrocopy	retro_dord_501 ,
Echinops telfairi	ENSETEG00000003242	1 retrocopy	retro_etel_2002,
Myotis lucifugus	ENSMLUG00000013128	1 retrocopy	retro_mluc_209,