RetrogeneDB ID: retro_dord_787

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_9831:10172..10575(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cenpk
• Ensembl ID: ENSDORG00000007357
• Aliases: None
• Description: centromere protein K [Source:MGI Symbol;Acc:MGI:1926210]

Sequence

>retro_dord_787
GTTGAGCAAGATCTAGATCCAGATAGTACTACAGGTACAGAATTTGTTATAGATTCTGAAGAAGAACTTATTAAAGAATG
TGAAGAACTCTGGAAAGATATGGAAAATTGTCCGAATAAATGGTTGCTTATTGGAACTGAGACACTCACCTAATTCAAAT
GCACAGCTATCATTACTGATGATGCAAGCGAAATGCTTGACTGCTGAATTCAAGCAATGGCAGAATGAAACACCTGAAGT
AATTCCTCTGACTGATGATGTTCTAACTACATTAGAGAAGGAAGAGTTACAAAAATTGAAAAATGATCTTGAAATTATAC
TACTCACTATTCAGTCCAAGAATAAAAAGTTAAAGGAAGACTTTGCAAGAGAGCAGCAGTGGTTGGATGAACAGCAACAA
ATA

Alignment

ORF - retro_dord_787 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.74 %
• Parental protein coverage: 50.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VEQDLDPDSTTGTEFVIDSEEELIKECEELWKDMEKCQNKWSLIGTETLT-NSNAQLSLLMMQVKCLTAE
          VEQDLDPDSTTG.................LWKDME.C.NKW.LIGTETLT.NSNAQLSLLMMQ.KCLTAE
Retrocopy VEQDLDPDSTTGXXXXXXXXXXXXXXXXXLWKDMENCPNKWLLIGTETLT>NSNAQLSLLMMQAKCLTAE

Parental  FKQWQNETPEVIPLTDDVLTTLGKEELQKLKHDLEIILPTIQSKNKKLKEDFAREQQWLDEQQQM
          FKQWQNETPEVIPLTDDVLTTL.KEELQKLK.DLEIIL.TIQSKNKKLKEDFAREQQWLDEQQQ.
Retrocopy FKQWQNETPEVIPLTDDVLTTLEKEELQKLKNDLEIILLTIQSKNKKLKEDFAREQQWLDEQQQI

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_787 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013993	1 retrocopy	retro_chof_1252,
Dipodomys ordii	ENSDORG00000007357	1 retrocopy	retro_dord_787 ,
Equus caballus	ENSECAG00000019165	1 retrocopy	retro_ecab_181,
Erinaceus europaeus	ENSEEUG00000005831	1 retrocopy	retro_eeur_81,
Monodelphis domestica	ENSMODG00000019645	1 retrocopy	retro_mdom_1446,
Oryctolagus cuniculus	ENSOCUG00000011568	2 retrocopies	retro_ocun_1199, retro_ocun_74,
Tursiops truncatus	ENSTTRG00000006527	1 retrocopy	retro_ttru_1310,