RetrogeneDB ID: retro_dord_611

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_40474:4..401(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BC026590
• Ensembl ID: ENSDORG00000008618
• Aliases: None
• Description: cDNA sequence BC026590 [Source:MGI Symbol;Acc:MGI:2677850]

Sequence

>retro_dord_611
TGCGTGTTATCACTGGCTGCTTCTCATCCAGTTCTTCAAAGCAGAAAAGAAAGTCAAAGCATTTCCTATTAGAGCAGTAC
AAAGTATAGCAGACTGCAGAAAAAATTTTCAGGAAATTTATGTGAGGCACACAGTTGTTAAGAAAATTCGCACTTCTGTG
TAAAATCTGCTGTTAGGACAAAGAATAAAGCATAGATAGCTATGTTTGCTAGAGGATGGCTGATGGAAGTGAATAGAAAC
ATTCTCCATTACCATCTATTCTTGAGAAAAGCTATCCACTGAGGGCTACATTGCAGTTATGTTACCCAAATTTGAAGAAT
GTAAAAGCATAACAGAAGGGCTACTGACACAAAAACAACACAAGCAATTCATAGTAAAATGAATTAATGCCACAACA

Alignment

ORF - retro_dord_611 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.23 %
• Parental protein coverage: 73.48 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  CVITLAASHPVLQSGKTIQSISYQISTNCSRLQNKVSG-KFKRGAQFLTELAPLCKIYCSDGE-EYTISS
          CV..LAASHPVLQS.K..QSISY..ST..SRLQ.K.SG.KF..G.Q.L...A.LCKI.C.D.E....I..
Retrocopy CVLSLAASHPVLQSRKESQSISY*SSTKYSRLQKKFSG<KFM*GTQLLRKFALLCKICC*DKE>KA*IAM

Parental  CIRGRLMEVNENILHK-PSILQ-EKPSTEGYIAVVLPKFEESKSITEGLLTQKQYDEIVGKRMDATT
          ..RG.LMEVN.NILH..PSIL..EK.STEGYIAV.LPKFEE.KSITEGLLTQKQ......K...ATT
Retrocopy FARGWLMEVNRNILHY<PSILE<EKLSTEGYIAVMLPKFEECKSITEGLLTQKQHKQFIVK*INATT

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_611 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 13 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004996	1 retrocopy	retro_btau_873,
Canis familiaris	ENSCAFG00000028510	1 retrocopy	retro_cfam_1345,
Cavia porcellus	ENSCPOG00000005927	1 retrocopy	retro_cpor_1488,
Dipodomys ordii	ENSDORG00000008618	1 retrocopy	retro_dord_611 ,
Homo sapiens	ENSG00000119328	1 retrocopy	retro_hsap_1197,
Macropus eugenii	ENSMEUG00000013637	1 retrocopy	retro_meug_1321,
Microcebus murinus	ENSMICG00000002074	1 retrocopy	retro_mmur_1363,
Monodelphis domestica	ENSMODG00000012563	1 retrocopy	retro_mdom_1837,
Oryctolagus cuniculus	ENSOCUG00000001882	1 retrocopy	retro_ocun_1527,
Otolemur garnettii	ENSOGAG00000024317	1 retrocopy	retro_ogar_1200,
Pongo abelii	ENSPPYG00000019483	1 retrocopy	retro_pabe_997,
Sorex araneus	ENSSARG00000009305	1 retrocopy	retro_sara_313,
Ictidomys tridecemlineatus	ENSSTOG00000027231	1 retrocopy	retro_itri_583,