RetrogeneDB ID: retro_dord_8

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_3716:265285..266614(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDORG00000007353
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDORG00000000123
• Aliases: None
• Description: None

Sequence

>retro_dord_8
TATGCATTAGACCCTTCACTGGCTAATCACCAAGTGTCTGCTAAGTATATTGGCTCTGTAGAGAAGGCTGAAAAAAATCA
AGGTTTAACCGTCTTTGAAACTGGCCAGAAGAAAACAGCAAAGAGGAAAAGGTTCAAAGAAAATGATGCATCTAATATTG
ATGGTTTCTCGGGACCATGGGCAAAATACGTGGATGAAAAAGATGTAGCTAAACCTTCAGACGAACAGCAACAAGAATTG
GATGAAATCACAGCAAAGAGGCAGAAAAAAGGCAAGCAGGAAGAGGAGAAACCTGGGGAAGAGAAAACAATCCTCCATGT
TAAAAATATGTACGACTATCAATGGAGGTCCTACCTTCACATACCTCAAGATGTTGGTGTTAATCTGAGGTCATCTGTAC
TGCCTGAAAAGTGTTACCTTCCCAAAAAACAAATTCATGTGTGGTCTGGACACACAAAGGGAGTCAGTGCAGTCAGATTG
TTTCCTCTCTCTGGCCATTTATTGCTGTCTTGTTCCATGGACTGTAAAATTAAGCTCTGGGAAGTTTATGGAGACCGGCG
TTGTCTGCGAACAGCTATTGGTCACAGCAAAGCTGTGAGAGACATCTGCTTCAACACTGCAGGAACACAGTTTCTTAGTG
CAGCCTATGACAGATATCTTAAACTCTGGGACACGGAGACAGGACAATGTCTATCAAGGTTTACAAACCAGAAAGTGCCC
TACTGTGTCAAATTCAATCCCGATGAAGATAAGCAAAATCTCTTCGTGGCTGGGATGTCTGATAAAAAGATTGTACAGTG
GGACATTCGAAGTGGACAAATTGTCCAAGAATATGACCGGCACTTGGGAGCTGTCAATGCCATTGTCTTTGTGGATGAGA
GTAGGAGATTTGTGAGCACATCTGATAAGAGCCTTAGGGTTTGGGAGTGGGGTATCCCTGTAGATTTCAAGTACATAGCA
GAGCCCAGCATGCATTCCATGCCTGCAGTGACTTTGTCTCCAAATGGAAAATGGTTAGCATGCCAGTCAATGGACAACCA
AATCTTAATTTTTGGAGCACAGAACAGATTCAGGTTAAATAAGAAAAAAGTTTTTAAGGGCCACATGGTTGCAGGCTATG
CTTGTCAGATAGACTTTTCACCAGACATGAGCTATGTAATTTCAGGAGATGGAGATGGAAAGTTAAACATCTGGGACTGG
AAGACTACAGAACTGTACAGTTGGTTTACAGCCCACGATGAGGTGTGCATCGGTGCAGTGTGGCTTCCTCACGAACCTTC
CAAAGTGATCACATGCGGGTGGGATGGTCTCATCAAACTGTGGGATTAA

Alignment

ORF - retro_dord_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.67 %
• Parental protein coverage: 57.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KEMYDYQGRSYLHIPQDVGVNLRSSVPPEKCYLPKKQIHVWSGHTKGVSAVRLFPLSGHLLLSCSMDCKI
          K.MYDYQ.RSYLHIPQDVGVNLRSSV.PEKCYLPKKQIHVWSGHTKGVSAVRLFPLSGHLLLSCSMDCKI
Retrocopy KNMYDYQWRSYLHIPQDVGVNLRSSVLPEKCYLPKKQIHVWSGHTKGVSAVRLFPLSGHLLLSCSMDCKI

Parental  KLWEVYGDRRCLRTFIGHSKAVRDICFNTAGTQFLSAAYDRYLKLWDTETXXXXXXXXN-RVPYCVKFNP
          KLWEVYGDRRCLRT.IGHSKAVRDICFNTAGTQFLSAAYDRYLKLWDTET........N..VPYCVKFNP
Retrocopy KLWEVYGDRRCLRTAIGHSKAVRDICFNTAGTQFLSAAYDRYLKLWDTETGQCLSRFTNQKVPYCVKFNP

Parental  DEDKQNLFVAGMSDKKIVQWDIRSGEIVQEYDRHLGAVNTIVFVDENRRFVSTSDDKSLRVWEWDIPVDF
          DEDKQNLFVAGMSDKKIVQWDIRSG.IVQEYDRHLGAVN.IVFVDE.RRFVSTSD.KSLRVWEW.IPVDF
Retrocopy DEDKQNLFVAGMSDKKIVQWDIRSGQIVQEYDRHLGAVNAIVFVDESRRFVSTSD-KSLRVWEWGIPVDF

Parental  KYIAEPSMHSMPAVTLSPNGKWLACQSMDNQILIFGAQNRFRLNKKKIFKGHMVAGYACQVDFSPDMSYV
          KYIAEPSMHSMPAVTLSPNGKWLACQSMDNQILIFGAQNRFRLNKKK.FKGHMVAGYACQ.DFSPDMSYV
Retrocopy KYIAEPSMHSMPAVTLSPNGKWLACQSMDNQILIFGAQNRFRLNKKKVFKGHMVAGYACQIDFSPDMSYV

Parental  ISGDGNGKLNIWDWKTTKLYSRFKAHDKVCIGAVWHPHETSKVITCGWDGLIKLWD
          ISGDG.GKLNIWDWKTT.LYS.F.AHD.VCIGAVW.PHE.SKVITCGWDGLIKLWD
Retrocopy ISGDGDGKLNIWDWKTTELYSWFTAHDEVCIGAVWLPHEPSKVITCGWDGLIKLWD

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_8 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000000123	1 retrocopy	retro_dord_8 ,
Oryctolagus cuniculus	ENSOCUG00000001223	1 retrocopy	retro_ocun_1587,