RetrogeneDB ID: retro_dord_715

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_60192:3817..4435(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDORG00000002845
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDORG00000004369
• Aliases: None
• Description: None

Sequence

>retro_dord_715
TACTGGTATTGTAAGAACAAACCATACCCAAAGCCTTGCTTTTGTCGAGGTGTCCCTGATGCTAAGATCCGCATCTTTGA
CCTGGGGGCAGAAGAAGGCAGAAGTGGATGAGTTCCCACTTTGTGGGCCCAAGGTATCAGATGCATATGAGCAGCTCTCC
TCTGAAGCCCTGGAGGCTGTGCGTATTTGTCCCAACAAGTGTATGGTAAAAAGTTGTGGCAAAATGGCTTTCATATTCGA
GTGTGACTGCATCCTTTCCACGTCATTCACATCAACAAGGTGTTGTCCTGCGCTGGGGCTGACAGGCTCTAGACAGGTAT
GCGGGGGTGCCTTTGGGAAGCCCCAGGACACTGTGGCCAGGGTTCACATTGGCCAGGTAATCACGTCCATCCGCACCAAG
CTGCAGAATAAAGAACATGTGATTGAGGCCTTACGCAGGGCCGAGTTCAAGTTCCCTGGTTGTCAGAAGATCCACATCTC
CAAGAAGTGGGGCTTTACCAAGTTCAACGTGGATGAGTTTGGAGACGTGGTAGCTGAGAAGCGCCTCATTCCTGATGGTG
TGGAGTCAAATACATCCCAAATCGTGGTCCTCTGGATACGTGGAGCCCCCTGCATTCC

Alignment

ORF - retro_dord_715 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 90.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  YRYCKNKPYPKSRFCRGVPDAKIRIFDLG-RKKAKVDEFPLCGHMVSDEYEQLSSEALEAARICANKYMV
          Y.YCKNKPYPK..FCRGVPDAKIRIFDLG..KKA.VDEFPLCG..VSD.YEQLSSEALEA.RIC.NK.MV
Retrocopy YWYCKNKPYPKPCFCRGVPDAKIRIFDLG>QKKAEVDEFPLCGPKVSDAYEQLSSEALEAVRICPNKCMV

Parental  KSCGK-DGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMR-GAFGKPQGTVARVHIGQVIMSIRTKLQNK
          KSCGK..GFHIRV.LHPFHVI.INK.LSCAGADRL.TGMR.GAFGKPQ.TVARVHIGQVI.SIRTKLQNK
Retrocopy KSCGK<NGFHIRV*LHPFHVIHINKVLSCAGADRL*TGMR>GAFGKPQDTVARVHIGQVITSIRTKLQNK

Parental  EHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADEFEDMVAEKRLIPDG-CGVKYIPNRGPLDKWRALHS
          EHVIEALRRA.FKFPG.QKIHISKKWGFTKFN.DEF.D.VAEKRLIPDG.CGVKYIPNRGPLD.W..LHS
Retrocopy EHVIEALRRAEFKFPGCQKIHISKKWGFTKFNVDEFGDVVAEKRLIPDG<CGVKYIPNRGPLDTWSPLHS

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_715 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 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000004369	2 retrocopies	retro_dord_14, retro_dord_715 ,
Echinops telfairi	ENSETEG00000001712	10 retrocopies	retro_etel_1073, retro_etel_1284, retro_etel_1517, retro_etel_1654, retro_etel_249, retro_etel_338, retro_etel_403, retro_etel_47, retro_etel_538, retro_etel_631,
Gorilla gorilla	ENSGGOG00000000131	4 retrocopies	retro_ggor_1873, retro_ggor_2425, retro_ggor_253, retro_ggor_61,
Macropus eugenii	ENSMEUG00000013163	3 retrocopies	retro_meug_1839, retro_meug_5, retro_meug_547,
Macaca mulatta	ENSMMUG00000005494	5 retrocopies	retro_mmul_1506, retro_mmul_1654, retro_mmul_307, retro_mmul_335, retro_mmul_906,
Monodelphis domestica	ENSMODG00000008731	2 retrocopies	retro_mdom_177, retro_mdom_829,
Tupaia belangeri	ENSTBEG00000003734	1 retrocopy	retro_tbel_61,
Tarsius syrichta	ENSTSYG00000004067	7 retrocopies	retro_tsyr_11, retro_tsyr_1644, retro_tsyr_1739, retro_tsyr_1986, retro_tsyr_559, retro_tsyr_640, retro_tsyr_960,
Tursiops truncatus	ENSTTRG00000011407	7 retrocopies	retro_ttru_1085, retro_ttru_122, retro_ttru_1226, retro_ttru_1437, retro_ttru_820, retro_ttru_858, retro_ttru_867,