RetrogeneDB ID: retro_dord_278

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_7:155150..156025(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDORG00000016474
• Aliases: None
• Description: None

Sequence

>retro_dord_278
ATGGCCACAATGGCGGCTGCCACTCTGCTGCGCGCAATGCCCCGCTATAGCGGTCTCTGCGCCAGTCCTACCCCATTGCT
GCATGGTCTGTTGCAGCCGCTGAGGACCCCGGCTTTGCTCCTCTTGTGTCGGGGCCTGGCCGTGGAAGCCAAGAAGGCCT
ATGGGTGAGACAAACCTCATGTGAACATGGGTACCATCGGCCATGTGGACCATGGCAAAACCACACTGACCGCCCCTATC
ACCAAAATTCTAGCAGAGGCAGATGGGGCGAAGTTCAAGAAGTATGAGGAGATTGACAATGCCCCAGGAGAGAGAGCTCA
GGGCATCACCATCAACGCTGCCCACGTGGAGTATAGCTCTGCTACCCGCCACTATGCCCACACAGACTGCCCAGGCCATG
CAGATTATGTTAAGAATATGATCACAGGTACTGCACCCTTGGATGGCAGCGTCTTGGTAGTGGCAGCAAATGATGGCCCC
ATGCCCCAGCCCCGAGAGCACTTCCTACTGGCCAAACAGATAGGGGTAGAGCATATTGTGGTGTACGTGAACAAGGCAGA
TGCAGTGCAGGACTTTTTGATGGTGGAGCTTGTGAAGCTGGAGATCCGGGAACTGCTCACCGAGTTCGTCTACAAAGGGG
AGGAGACCCCAGTCATCGTAGGCTCTGCTCTCTGTGCCCTTGAGCTACGTGACCCTGAGCGAGGAGTGAGTCAGTGCAGA
AGCTGCTGGATGCTATGAACACTTACATCCCAGTGCCCACCTGGGACCTAGAGAAGCCTTTCCTGTTGCCTGTGGAATCT
GTTTACTCTATTCCTGGCCAGGGCACAGTGGTGACAGGTACATTGGAGCATGGCATTTTGAAGAAGGGAGATGAA

Alignment

ORF - retro_dord_278 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.4 %
• Parental protein coverage: 64.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MATMAAATLLRATPRLSGLRASPTPWPHGLLRPLRTPAWPLLCRGLAVEAKKAYVRDKPHVNVGTIGHVD
          MATMAAATLLRA.PR.SGL.ASPTP..HGLL.PLRTPA..LLCRGLAVEAKKAY..DKPHVN.GTIGHVD
Retrocopy MATMAAATLLRAMPRYSGLCASPTPLLHGLLQPLRTPALLLLCRGLAVEAKKAYG*DKPHVNMGTIGHVD

Parental  HGKTTLTAAITKILAEGGGAKFKKYEEIDNAPEERARGITINAAHVEYSTATRHYAHTDCPGHADYVKNM
          HGKTTLTA.ITKILAE..GAKFKKYEEIDNAP.ERA.GITINAAHVEYS.ATRHYAHTDCPGHADYVKNM
Retrocopy HGKTTLTAPITKILAEADGAKFKKYEEIDNAPGERAQGITINAAHVEYSSATRHYAHTDCPGHADYVKNM

Parental  ITGTAPLDGCILVVAANDGPMPQTREHLLLAKQIGVEHIVVYVNKADAVQDSEMVELVELEIRELLTEFG
          ITGTAPLDG..LVVAANDGPMPQ.REH.LLAKQIGVEHIVVYVNKADAVQD..MVELV.LEIRELLTEF.
Retrocopy ITGTAPLDGSVLVVAANDGPMPQPREHFLLAKQIGVEHIVVYVNKADAVQDFLMVELVKLEIRELLTEFV

Parental  YKGEETPVIVGSALCALEQRDPELGV-KSVQKLLDAVDTYIPVPTRDLEKPFLLPVESVYSIPGRGTVVT
          YKGEETPVIVGSALCALE.RDPE.GV..SVQKLLDA..TYIPVPT.DLEKPFLLPVESVYSIPG.GTVVT
Retrocopy YKGEETPVIVGSALCALELRDPERGV<ESVQKLLDAMNTYIPVPTWDLEKPFLLPVESVYSIPGQGTVVT

Parental  GTLERGILKKGDE
          GTLE.GILKKGDE
Retrocopy GTLEHGILKKGDE

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_278 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 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000016474	1 retrocopy	retro_dord_278 ,
Homo sapiens	ENSG00000178952	1 retrocopy	retro_hsap_1816,
Macropus eugenii	ENSMEUG00000011131	1 retrocopy	retro_meug_1783,
Monodelphis domestica	ENSMODG00000015564	1 retrocopy	retro_mdom_384,
Mus musculus	ENSMUSG00000073838	1 retrocopy	retro_mmus_10,
Ornithorhynchus anatinus	ENSOANG00000013114	1 retrocopy	retro_oana_36,
Oryctolagus cuniculus	ENSOCUG00000002683	1 retrocopy	retro_ocun_333,
Pan troglodytes	ENSPTRG00000007939	1 retrocopy	retro_ptro_1174,
Rattus norvegicus	ENSRNOG00000018604	1 retrocopy	retro_rnor_1134,
Vicugna pacos	ENSVPAG00000009541	1 retrocopy	retro_vpac_346,
Drosophila melanogaster	FBgn0033184	1 retrocopy	retro_dmel_52,