RetrogeneDB ID: retro_dord_22

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_147337:512..1451(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDORG00000004462
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDORG00000013870
• Aliases: None
• Description: None

Sequence

>retro_dord_22
GAGATTTCGATGGAGAAGGTGAAGGTGAAACGTTATGTGTCAGGAAGGAGGCCAGACTATGCCCCCATGGAGGCCTCAGA
TGAGGAGGACAAAGACTTTCAATTCTTTAAGAAAGCCAAAGAACAAGACGCTGAGCCAGAGAAACGCAAGGAAGACTCCT
TGAGGGACCCTCGTCTGCGGAGCCTACAACATCTGATCCGTGAAGCTGCGGAAGAGAGAATGGCTCAACATCGGAAGATG
GCGGCACTTGACATGGTAGGCCAAAGTGACTCAGAAGGACAAGGAGATGGCAGAGAAGGAGAGGAAGAAGAAATGGACGA
TGAGGAAATAGAACGGCACCGTGGCCTGCTGCGTCAGAGAGCCAAGGAAAGGAAACATGAAGAGATGGAGGTCATGGAGG
CCGGAGAGGATCGGCATTCTGGACACGAGTCAGAATCTGAGTGTGACTATGAAGAGTATACAGGCAGTGAAGATGAGATG
GAGCCTCACTGGAAGCCACTTTTCATTCAAAGGAAGGACCGAGTGACAGTTCAAACATGGAAGGTCCAAGCACTGAAACA
CAAGGAGTTGGAGCAGGAAGCAAAACGCTCGGCTGAAAAGAGACACAGGTACACACTTCAGATTGTAGAGGAGGAGGCCA
AGAGGGAGCTGGGGAAGAACAGAGGGTCCCTGGCTGCACTGGATGCTCTCCATACTGAGGAGGAAAATGAGGAGGAATAT
GAGGCATGGAAAGTTCGAGAGTTCAAAAGAATCAAGAGGGACCGAGAAGGTCGAGAAGCCCTTGCAAAGGAGAAAGCAGA
AACTGAACGCCTGCGAAACCTGACTGAGGAGGGGAGGCGAGCTGAGCTTCGGGCCAAGGCCCAAGTCCTTAGCAACAAAG
CGGTTCAAGGCAAGTACAAGTTTTTACAGAAGTATTATCACCGAGGTGCTTTCTTCATG

Alignment

ORF - retro_dord_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.44 %
• Parental protein coverage: 73.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EISMEKVKVKRYVSGKRPDYAPMESSDEEDEDFQFINKKELDAESEELEEDSSSDSHLRRLQTVISENVE
          EISMEKVKVKRYVSG.RPDYAPME.SDEED.DFQF..K....A.....E........LR...........
Retrocopy EISMEKVKVKRYVSGRRPDYAPMEASDEEDKDFQFFKK----AKEQDAEPEKRKEDSLRDPRLRSLQHLI

Parental  KRLARHRKVEPEVVGESDSEVEGDAWRMEREDSSEEEEEEIDDEEIERRRGMMRQRAQERKNEEMEVMEV
          ...A..R..........D.....D.......D..E.EEEE.DDEEIER.RG..RQRA.ERK.EEMEVME.
Retrocopy REAAEERMAQHRKMAALDMVGQSDS--EGQGDGREGEEEEMDDEEIERHRGLLRQRAKERKHEEMEVMEA

Parental  EDEGRSGEESESESEYEEYTDSEDEMEPRLKPVFIRKKDRVTVQEREAEALKQKELEQEAKRLAEERRKY
          .....SG.ESESE..YEEYT.SEDEMEP..KP.FI..KDRVTVQ.....ALK.KELEQEAKR.AE.R..Y
Retrocopy GEDRHSGHESESECDYEEYTGSEDEMEPHWKPLFIQRKDRVTVQTWKVQALKHKELEQEAKRSAEKRHRY

Parental  TLKIVEEETKKELEENKRSLAALDALNTDDENDEEEYEAWKVRELKRIKRDREDREALEKEKAEIERMRN
          TL.IVEEE.K.EL..N..SLAALDAL.T..EN.EEEYEAWKVRE.KRIKRDRE.REAL.KEKAE.ER.RN
Retrocopy TLQIVEEEAKRELGKNRGSLAALDALHTEEEN-EEEYEAWKVREFKRIKRDREGREALAKEKAETERLRN

Parental  LTEEERRAELRANGKVITNKAVKGKYKFLQKYYHRGAFFM
          LTEE.RRAELRA...V..NKAV.GKYKFLQKYYHRGAFFM
Retrocopy LTEEGRRAELRAKAQVLSNKAVQGKYKFLQKYYHRGAFFM

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_22 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 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000013870	1 retrocopy	retro_dord_22 ,
Myotis lucifugus	ENSMLUG00000013000	2 retrocopies	retro_mluc_1384, retro_mluc_2298,
Mus musculus	ENSMUSG00000048222	2 retrocopies	retro_mmus_1147, retro_mmus_2346,
Mus musculus	ENSMUSG00000068479	2 retrocopies	retro_mmus_2386, retro_mmus_2638,
Otolemur garnettii	ENSOGAG00000010206	1 retrocopy	retro_ogar_1784,
Rattus norvegicus	ENSRNOG00000015984	1 retrocopy	retro_rnor_83,
Sarcophilus harrisii	ENSSHAG00000014628	1 retrocopy	retro_shar_107,
Ictidomys tridecemlineatus	ENSSTOG00000006967	2 retrocopies	retro_itri_1105, retro_itri_1494,
Tupaia belangeri	ENSTBEG00000005050	2 retrocopies	retro_tbel_3001, retro_tbel_3246,