RetrogeneDB ID: retro_dord_128

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_3716:297813..298434(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ik
• Ensembl ID: ENSDORG00000006584
• Aliases: None
• Description: IK cytokine [Source:MGI Symbol;Acc:MGI:1345142]

Sequence

>retro_dord_128
ATGTCAAGAGAGTACAATGAGGATGAAGATCCAGCTGCCCGAAGGAGAAAAAAGAGAAGTTATTATGCTAAGTTACGCCA
ACAAGAAATTGAGAGAGCGAGCGAGCTAGCAGAGAAGTACCGGGACCGTGCCAAGGAACGAAGAGATGGTGTGAAGAAAG
ATTATGAGGAAACCAAGCCGATTAGCACCGCAGCCAACTATAGGGTTGTGGGCCCCACAGCAGAGGTGGACAAATCAGCT
GCAGAGAAAAGACAGTTGATCCAGGAGTCCAAATTTTTGGGTGGTGACATGGAGCACACCCACTTGGTCAAAGGCTTGGA
TTTTGCTCTACTTCAAAAGGTACGAGCTGAGATTGCCAGCAAAGAGGAAGAGGAATTGATGGAGAAACCTCAAAAGGAAA
CCAAGAAAGATGAGGATCCTGAGAACAAAATTGAATTTAAAACTCGTCTTGGCCGCAATGTGTATCATACGCTTTTTAAG
AGCAAAGCCGATGAGCGGAATGAGCTGTTCTTGCCAGGCCGCATGGCCTATGTGGTGGACCTGGACGATGAGTATGGGGA
TACAGATATTCCCACCACACTTATCCGTAGCAAGGCTGATTGCCCAACCGTGGAGGCCCAG

Alignment

ORF - retro_dord_128 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.43 %
• Parental protein coverage: 53.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPREYNEDEDPAARRRKKKSYYAKLRQQEIERERELAEKYRDRAKERRDGVNKDYEETELISTTANYRAV
          M.REYNEDEDPAARRRKK.SYYAKLRQQEIER..ELAEKYRDRAKERRDGV.KDYEET..IST.ANYR.V
Retrocopy MSREYNEDEDPAARRRKKRSYYAKLRQQEIERASELAEKYRDRAKERRDGVKKDYEETKPISTAANYRVV

Parental  GPTAEADKSAAEKRRQLIQESKFLGGDMEHTHLVKGLDFALLQKVRAEIASKEKEEEELMEKPQKETKKD
          GPTAE.DKSAAEKR.QLIQESKFLGGDMEHTHLVKGLDFALLQKVRAEIAS..KEEEELMEKPQKETKKD
Retrocopy GPTAEVDKSAAEKR-QLIQESKFLGGDMEHTHLVKGLDFALLQKVRAEIAS--KEEEELMEKPQKETKKD

Parental  EDPENKIEFKTRLGRNVYRMLFKSKAYERNELFLPGRMAYVVDLDDEYADTDIPTTLIRSKADCPTMEAQ
          EDPENKIEFKTRLGRNVY..LFKSKA.ERNELFLPGRMAYVVDLDDEY.DTDIPTTLIRSKADCPT.EAQ
Retrocopy EDPENKIEFKTRLGRNVYHTLFKSKADERNELFLPGRMAYVVDLDDEYGDTDIPTTLIRSKADCPTVEAQ

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_128 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 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009727	3 retrocopies	retro_dnov_618, retro_dnov_714, retro_dnov_960,
Dipodomys ordii	ENSDORG00000006584	4 retrocopies	retro_dord_128 , retro_dord_130, retro_dord_134, retro_dord_139,
Homo sapiens	ENSG00000113141	1 retrocopy	retro_hsap_2262,
Gorilla gorilla	ENSGGOG00000013374	1 retrocopy	retro_ggor_1685,
Loxodonta africana	ENSLAFG00000008152	1 retrocopy	retro_lafr_362,
Otolemur garnettii	ENSOGAG00000014281	1 retrocopy	retro_ogar_1402,
Pongo abelii	ENSPPYG00000015861	1 retrocopy	retro_pabe_1954,
Sorex araneus	ENSSARG00000007388	3 retrocopies	retro_sara_416, retro_sara_419, retro_sara_558,