RetrogeneDB ID: retro_dord_334

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_12567:8324..9242(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Abcf2
• Ensembl ID: ENSDORG00000012672
• Aliases: None
• Description: ATP-binding cassette, sub-family F (GCN20), member 2 [Source:MGI Symbol;Acc:MGI:1351657]

Sequence

>retro_dord_334
GTGGATTTGCTGACCAACGAGCTAGAGGACTTTGAGATGAAGAAAGCTACTGCTCGAGCTGTCACTGGCATCCTGGCTTT
TCACCCCAATAGTACCGACGTCCACATCATCAGCCTCTCACTCACCTTCCATGGTCAGGAGCTGCTCAGCAACACCAAAC
TGGAACTAAATTTTGGCCGTTATTATGGCCTCTTTGGCTTAAATGGAATCGGGAAGTCCATGCTGCTGTCTGCAATCGGG
AAGCATGAAGTGGCCATCCCTGAGCACATCGACATCTACCATCTGACCTGTGAGATGCCCCCTAGGGACAAGACCCCTTT
GCAGTGTGTGATGGAAGTGGACACAGAGCATGCCATGCTGGAGAGGGAGACTGAGCGGCTGGCTCACAAGGACGCGGAGT
GTGAGAAGCTCATGGAACTATACGAGTGCCTGGAGGAGCTGGATACCAACAAGGCAGAGATGAGGGCCTTATGGATTTGG
CATGGACTTGGTTTCACAGCTGCTATGCAGCACAAGAAGGTAAAAGACTTCAATGGGAGCTGGAGGATGAGGGTTGCCTT
AGCCAGAGCCCTCTTCATCCGGCCATTCATGCTGCTTCTGGACAAACCCACCAACCATTTGGACCTAGATGCTTGTGTAT
GGTTGGAAGAAGAACTAAAGACTTTTAAACATATCCTGGTCCTCGTGTCACACTCTCAGGATTTCCTGAATGGTGTCTGC
ACCAATATCATCCATATGCACAACAAGAAACTCGAGTATTATAGGGGTAATTATGATCAGTATGTGAAGACACGGCTGGA
GCTGGAGGAAAACCAGATGAAGAAGTTTCACTGGGAGCAAGACCAGATTGCACATATGAAGAACTATATTGCTAGATTTG
ATCATGGGTCCACCAAGTTGGCTCAGCAGACCCAGAGC

Alignment

ORF - retro_dord_334 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.91 %
• Parental protein coverage: 53.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VDLLTKELEDFELKKAAARAVTGVLASHPNSTDVHIINLSLTFHGQELLSDTKLELNSGRRYGLIGLNGI
          VDLLT.ELEDFE.KKA.ARAVTG.LA.HPNSTDVHII.LSLTFHGQELLS.TKLELN.GR.YGL.GLNGI
Retrocopy VDLLTNELEDFEMKKATARAVTGILAFHPNSTDVHIISLSLTFHGQELLSNTKLELNFGRYYGLFGLNGI

Parental  GKSMLLSAIGKREVPIPEHIDIYHLTREMPPSDKTPLQCVMEVDTERAMLEREAERLAHEDAECEKLMEL
          GKSMLLSAIGK.EV.IPEHIDIYHLT.EMPP.DKTPLQCVMEVDTE.AMLERE.ERLAH.DAECEKLMEL
Retrocopy GKSMLLSAIGKHEVAIPEHIDIYHLTCEMPPRDKTPLQCVMEVDTEHAMLERETERLAHKDAECEKLMEL

Parental  YERLEELDADKAEMRASRILHGLGFTPAMQRKKLKDFSGGWRMRVALARALFIRPFMLLLDEPTNHLDLD
          YE.LEELD..KAEMRA..I.HGLGFT.AMQ.KK.KDF.G.WRMRVALARALFIRPFMLLLD.PTNHLDLD
Retrocopy YECLEELDTNKAEMRALWIWHGLGFTAAMQHKKVKDFNGSWRMRVALARALFIRPFMLLLDKPTNHLDLD

Parental  ACVWLEEELKTFKRILVLVSHSQDFLNGVCTNIIHMHNKKLKYYTGNYDQYVKTRLELEENQMKRFHWEQ
          ACVWLEEELKTFK.ILVLVSHSQDFLNGVCTNIIHMHNKKL.YY.GNYDQYVKTRLELEENQMK.FHWEQ
Retrocopy ACVWLEEELKTFKHILVLVSHSQDFLNGVCTNIIHMHNKKLEYYRGNYDQYVKTRLELEENQMKKFHWEQ

Parental  DQIAHMKNYIARFGHGSAKLARQAQS
          DQIAHMKNYIARF.HGS.KLA.Q.QS
Retrocopy DQIAHMKNYIARFDHGSTKLAQQTQS

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_334 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004830	1 retrocopy	retro_cfam_1612,
Callithrix jacchus	ENSCJAG00000020371	3 retrocopies	retro_cjac_1859, retro_cjac_3526, retro_cjac_381,
Dipodomys ordii	ENSDORG00000012672	1 retrocopy	retro_dord_334 ,
Echinops telfairi	ENSETEG00000008032	2 retrocopies	retro_etel_1041, retro_etel_1058,
Macaca mulatta	ENSMMUG00000006679	1 retrocopy	retro_mmul_1414,
Oryctolagus cuniculus	ENSOCUG00000000245	1 retrocopy	retro_ocun_765,