RetrogeneDB ID: retro_dord_304

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_10811:228..1109(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDORG00000014493
• Aliases: None
• Description: None

Sequence

>retro_dord_304
AAGAATGTTCCTTTTAAAATTGTCTGGGCCTCTAATGGTGATGCCTGGGTTGAGGCTCATGGAAAATTCTATTCTCCGAG
CCAAATTGGAGCATTTGTGTTATGAAGATGAAAGAAACTGCAGAAAATTATTTGGGACATGCAGCAAAAAATGCTATGAT
TACCGTCCCTGCTTATTTCAATGATTCACAGAGACAGGCCACTAAGGATGCTGGCCAGATATCAGGACTAAATGTGCTTT
GGGTGATTAATGAAGCCACAGCTGCTGCTCTGGCCTGTGGTCTAGACAAATCTGAAGACAAAGTCATTGCTGTGTATGAT
TTAGGTGGTGGAATTTTTGATATTTCTGTCCTGGAAATTCAGAAAGGCGTATCTAAGGTGAAATCCACCAATGGGAATAC
TTTCTTAGGTGGTGAAGACTTTGATCACATTGTAAAGGAATTCAAGAAAGAGACAGTGGTTGATTTTACCAAAGACAACA
CAGCACTTCAGAGGGTACAGAAAGCCACTGAGGAGCTAAGCGTGAACTCTCTTCATCTATGCAGACTGACATTAACTTGC
CCTATCTGACTATGGATGCTTCTGGACCTAAGCATTTGAATATGAAGCTGACATGGGCTCAATTTGAGGGAATCGTCACT
GATCTTATCAAGAGGACTATTGCTCCTTGCCAGAAAGCTATAAAGGGTGCAGAAGTCACCAAGAGTGATATAGGAGAAGT
GATCCTTATTGGTGACATGACTAGGATGCCTAAGGTTCAGCAGACTGCAAGATCTTTTTGGCTGAGCCCCAAGTAAAGCT
GTTAATCCTGATGAGGCTGTGGCCATTGGAGGTGCCATTCAGGGAGGTTTGTTAGCTGGTGAAGTCACAGATGTGCTACT
C

Alignment

ORF - retro_dord_304 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.5 %
• Parental protein coverage: 59.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KNVPFKIVRASNGDAWVEAHGKLYSPSQIGAFVL-MKMKETAENYLGHAAKNAVITVPAYFNDSQRQATK
          KNVPFKIV.ASNGDAWVEAHGK.YSPSQIGAFVL.MKMKETAENYLGHAAKNA.ITVPAYFNDSQRQATK
Retrocopy KNVPFKIVWASNGDAWVEAHGKFYSPSQIGAFVL<MKMKETAENYLGHAAKNAMITVPAYFNDSQRQATK

Parental  DAGQISGLNVLRVINEPTAAALAYGLDKSEDKVIAVYDLGGGTFDISVLEIQKGVFEVKSTNGDTFLGGE
          DAGQISGLNVL.VINE.TAAALA.GLDKSEDKVIAVYDLGGG.FDISVLEIQKGV..VKSTNG.TFLGGE
Retrocopy DAGQISGLNVLWVINEATAAALACGLDKSEDKVIAVYDLGGGIFDISVLEIQKGVSKVKSTNGNTFLGGE

Parental  DFDQALLRHIVKEFKRETGVDLTKDNMALQRVREAAEK-AKCELSSSVQTDINLPYLTMDASGPKHLNMK
          DFD........KE....T.VD.TKDN.ALQRV..A.E..AK.ELSSS.QTDINLPYLTMDASGPKHLNMK
Retrocopy DFDH-IVKEFKKE----TVVDFTKDNTALQRVQKATEE<AKRELSSSMQTDINLPYLTMDASGPKHLNMK

Parental  LTRAQFEGIVTDLIKRTIAPCQKAMQDAEVTKSDIGEVILVGGMTRMPKVQQTVQDLFGRAP-SKAVNPD
          LT.AQFEGIVTDLIKRTIAPCQKA...AEVTKSDIGEVIL.G.MTRMPKVQQT....F...P.SKAVNPD
Retrocopy LTWAQFEGIVTDLIKRTIAPCQKAIKGAEVTKSDIGEVILIGDMTRMPKVQQTARS-FWLSP>SKAVNPD

Parental  EAVAIGAAIQGGVLAGDVTDVLL
          EAVAIG.AIQGG.LAG.VTDVLL
Retrocopy EAVAIGGAIQGGLLAGEVTDVLL

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_304 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000014493	1 retrocopy	retro_dord_304 ,
Macropus eugenii	ENSMEUG00000016000	1 retrocopy	retro_meug_953,
Ornithorhynchus anatinus	ENSOANG00000002817	1 retrocopy	retro_oana_82,
Tupaia belangeri	ENSTBEG00000015361	1 retrocopy	retro_tbel_2365,
Tarsius syrichta	ENSTSYG00000011769	1 retrocopy	retro_tsyr_2147,
Vicugna pacos	ENSVPAG00000006332	1 retrocopy	retro_vpac_524,