RetrogeneDB ID: retro_dord_197

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_5158:31949..32945(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDORG00000019810
• Aliases: None
• Description: None

Sequence

>retro_dord_197
ATGAATCTTTCACTGTTCCTCGCTGCCTTTTGCTTGGGAATAGCCTCAGCTACTCCAAAACATGACCAGAACTTAGACAC
AAAGTGGTACCAGTGGAAGTCAATGCACAGGAGACTATATGGCTCGAATGAAGAAGGATGGAGGAGAGCAGTCTGGGAAA
AGAACATGAAATTGATTGAAATTCATAAGGGGGAATACAGCCTAGGCAGACATGGTTTCACCATGAAAATGAACGTCTTT
GGGGACATGACCAATGAAGAATTCAGACAGGTGATGAATGACTTTCAGAATTCAAAGCACAAGAAGGGGAAAATGTTTCA
GGAACTTCTATTTTTTAAGCCCCCTGAATCTGTGAATTGGACAGAAAAAGGCTATGTGACCCCTGTGAAGAACCAGGGTC
AGTGTGGTTCTTGTTGGGCTTTCAGTGCGACTGGAGCCCTGGAAGGACAGATGTTCCAGAAGACTGGCAAACTGATTGCC
CTCAGTGAGCAGAACCTAGTGGACTGCTCTTATCCTCAAGGCAATCAGGGCTGCAACGGTGGCTTAATGGACTTTGCCTT
CCAGTATGTCAAGGAAGATAAAGGCTTGGACTCTGAGAAATCCTATCCATATGAAGCCCAGGATGGTAAGTGTAAGTACA
ATCCTGAATATGCTGTGGCAAATGACACTGGATTTGTGGACATCCCTCCGAGGGAGAAGTCCCTGCTGAAGGCAGTGGCC
TCTGTGGGGCCCATTTCTGCAGCTATGGATGCAAGCCATACATCCTTCCAGTTCTATGAATCAGGCATTTATTATGAACC
AAATTGTAGCAGCAAGGACCTGGATCACGGCATTCTGATTGTCGTCTACAGTGCTGATGGAAATGGCCCAGATGATAAAT
ATTGGCTTGTGAAGAACATCTGGGGTGCTCAATGGGGTACAGAAGGCTTCGTCAAAATAGCCAGGGACAGAGACAACCAC
TGTGGACTTGCAACTGCAGCTAGCTACCCCACAGTA

Alignment

ORF - retro_dord_197 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.03 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDPSLLLAILCLGMASAAPVLDPSLDAQWTKWKTEYGKSYHSDEEGWRRAIWEENWKMIEVHNEEERQGK
          M..SL.LA..CLG.ASA.P..D..LD..W..WK......Y.S.EEGWRRA.WE.N.K.IE.H..E...G.
Retrocopy MNLSLFLAAFCLGIASATPKHDQNLDTKWYQWKSMHRRLYGSNEEGWRRAVWEKNMKLIEIHKGEYSLGR

Parental  HTYTLEMNAFGDMTDEELQQGETEFQPVRPNEEEQIYPDLLFGDLPAFVDWREKGYVTHVKDQGQCNSCW
          H..T..MN.FGDMT.EE..Q....FQ.............LLF...P..V.W.EKGYVT.VK.QGQC.SCW
Retrocopy HGFTMKMNVFGDMTNEEFRQVMNDFQNSK-HKKGKMFQELLFFKPPESVNWTEKGYVTPVKNQGQCGSCW

Parental  AFCANGALEGQMFKKTGKLVSLSEQNLVDCSRPQNN-GCTGGLPHLAYQYVKNNRGLASEESYPYEAKNG
          AF.A.GALEGQMF.KTGKL..LSEQNLVDCS.PQ.N.GC.GGL...A.QYVK...GL.SE.SYPYEA..G
Retrocopy AFSATGALEGQMFQKTGKLIALSEQNLVDCSYPQGNQGCNGGLMDFAFQYVKEDKGLDSEKSYPYEAQDG

Parental  PCRYKPENSAANVTGYVILPPGEQALMRAVATVGPIATGFHSAHSSFKYYKGGIHYNPTC-PKYLTHGVV
          .C.Y.PE...AN.TG.V..PP.E..L..AVA.VGPI.......H.SF..Y..GI.Y.P.C..K.L.HG..
Retrocopy KCKYNPEYAVANDTGFVDIPPREKSLLKAVASVGPISAAMDASHTSFQFYESGIYYEPNCSSKDLDHGIL

Parental  VVGYGYEGEEETENNKYWLIKNSYGTNWGINGYAKVARDRNNHCGIASFSLYPTV
          .V.Y...G.......KYWL.KN..G..WG..G..K.ARDR.NHCG.A....YPTV
Retrocopy IVVYSADG--NGPDDKYWLVKNIWGAQWGTEGFVKIARDRDNHCGLATAASYPTV

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_197 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 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000019810	1 retrocopy	retro_dord_197 ,
Macropus eugenii	ENSMEUG00000002168	2 retrocopies	retro_meug_1349, retro_meug_1567,
Macropus eugenii	ENSMEUG00000014293	1 retrocopy	retro_meug_1873,
Macropus eugenii	ENSMEUG00000016209	2 retrocopies	retro_meug_159, retro_meug_1727,
Myotis lucifugus	ENSMLUG00000003975	1 retrocopy	retro_mluc_2231,
Myotis lucifugus	ENSMLUG00000025440	1 retrocopy	retro_mluc_2399,
Macaca mulatta	ENSMMUG00000013861	1 retrocopy	retro_mmul_1669,
Monodelphis domestica	ENSMODG00000002844	1 retrocopy	retro_mdom_1101,
Petromyzon marinus	ENSPMAG00000003453	1 retrocopy	retro_pmar_7,
Tarsius syrichta	ENSTSYG00000002858	2 retrocopies	retro_tsyr_150, retro_tsyr_603,