RetrogeneDB ID: retro_dord_612

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_40619:3001..4678(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pogk
• Ensembl ID: ENSDORG00000006822
• Aliases: None
• Description: pogo transposable element with KRAB domain [Source:MGI Symbol;Acc:MGI:1918842]

Sequence

>retro_dord_612
GTTTCAGCCCTATTTGATGAGGTGGCCATATATTTTTCTGATGAGGAGTGGGAAGTTTTGACGGACCAACAAAAGGCCCT
CTACCGGAAAGTCATGAGGATGAATTATGAAACTATTCTGTCCCTGGAATTACCATTTCCTAAGCCAGACATGATCACTC
GTTTGGAACGGGAGGAAGAGTCTCATAATTCTGATGAGTGGCAGCTACAAGGAGGACCCGTTACAGAAAATGAAGAATCT
GATGTAAAGCCTCCAGATTGGGCGACCCCAATGAATACCACCTCCCACTTCCCTCTGTCTCAGCATCTTGACAGCTTTGG
CCTGCACCTGCCTCGGGACATCACTGAGCTGCCTGAATGGAGTGAGGGGTATCCCTTCTGCATGGCCATGGGCTTCCCGG
GATACGAACTCTCGGCTGATGACATAGCTGGGAAGTTTCAGTTCAGCCGGGGATGTGCCGCAGTTAAGATGCAGGATTCA
AGTTGATGGTGGTAGAGTATGCCGAGAGCACCAACAACTGCCAGGCTGCCAAGCAGTTTGGAGTATTCGAAAAAACATTT
GAGACTGGCGCAAGGTGAAGCCACAGCTGCAGAATGCCCATGCCATGCGACGGGCATTCCGAGGTCCCAAGAATGGCAGG
TTTGCTTTGGTGGACCAACGCGTGGCTGAGTATGTCAGATACATGCAGGCCAAAGGGGACCCCATAACCAGGGAGGCGAT
GCAGCTGAAAGCTCTTGAAATTGCCCAAGAAATGAACATTCCAGAGAAAGGGTTTAAAGCAAGCTTGGGTTGGTGTCGAA
GAATGATGAGAAGGTATGACCTGTCTCTGAGGCACAAAGTACCTGTACCCCAGCACCTGCCTGAAGACCTGACTGAGAAG
CTCATCACTTACCAGCAGACTGTGTTATCTCTGCGCAGGGCGCATGACTACGAGGTGACACAGATGGGGAATGCAGACGA
GACACCCATCTGTTTGGAGGTGCCATCCAGGGTTACTGTTGACAACCAGGGTGAAAAGCCTGTGTTGGTCAAAACTCCAG
GCAGGGAGAAACTAAGGATCACTGCCATGCTTGGTGTCTTGGCTGATGGGAAGAAGTTACCTCCGTATATCATTTTGAGG
GGAACCTACATCCCCCCGGGAAAGTTCCCCAGTGGGATGGAAATCCGCTGCCATTGCTATGGGTGGATGACTGAAGACTT
GATGCAGGACTGGTTGGAAGTGGTGTGGAAACGCAGGACAGGAGCACTTCCCAAGCAACGAGGGGTGCTGATCCTGAATG
GCTTCCGGGGTCATGCCACTGATTCTGTGAAGAATCTGAACACGGACATGGTGATCATCCCCGGGAGCCTAACCCCACAG
CTGCAGGTGCTGGATGTGGTGGTCTACAAGCCATTGAATGACAGTGTGCGTGCCCAGTACTATAACTGGCTTTTGGTTGG
GAACCTGGCGCTCAGCCCCACTGGGAATTCCAAGAAGTCACCCCTGGGTCTCTTCCTGGAATGGGTCATGGTGGCATGGA
ACAGCATCTCAAGTGAATCCATTGTCCAAGGGTTCAAGTGCCACATCTCCAGCAACTTGGAGGAGGAAGATGACGAACTG
TGGGAAATCGAAGTGAGTTGCCAGGAGGAGGGGAACCACCGAAAGAATGTGATATTGAGAGCATGACTGAGGGCAAC

Alignment

ORF - retro_dord_612 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.37 %
• Parental protein coverage: 92.78 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VPALFDEVAIYFSDEEWEVLTDQQKALYREVMRMNYETVLSLEFPFPKPDMITRLEREEESHNSEEWQLQ
          V.ALFDEVAIYFSDEEWEVLTDQQKALYR.VMRMNYET.LSLE.PFPKPDMITRLEREEESHNS.EWQLQ
Retrocopy VSALFDEVAIYFSDEEWEVLTDQQKALYRKVMRMNYETILSLELPFPKPDMITRLEREEESHNSDEWQLQ

Parental  GGPVTENEESDVKSPDWATPMNTTSHFPQPQHLDSFGLRLPRDITELPEWSEGYPFCMAMGFPGYDLSAD
          GGPVTENEESDVK.PDWATPMNTTSHFP..QHLDSFGL.LPRDITELPEWSEGYPFCMAMGFPGY.LSAD
Retrocopy GGPVTENEESDVKPPDWATPMNTTSHFPLSQHLDSFGLHLPRDITELPEWSEGYPFCMAMGFPGYELSAD

Parental  DIAGKFQFSRG-MRRSYDAGFKLMVVEYAESTNNCQAAKQFGVFEK-NVRDWRKVKPQLQNAHAMRRAFR
          DIAGKFQFSRG.M.RS.DAGFKLMVVEYAESTNNCQAAKQFGVFEK.N..DWRKVKPQLQNAHAMRRAFR
Retrocopy DIAGKFQFSRG<MCRS*DAGFKLMVVEYAESTNNCQAAKQFGVFEK<NI*DWRKVKPQLQNAHAMRRAFR

Parental  GPKNGRFALVDQRVAEYVRYMQAKGDPITREAMQLKALEIAQEMNIPEKGFKASLGWCRRMMRRYDLSLR
          GPKNGRFALVDQRVAEYVRYMQAKGDPITREAMQLKALEIAQEMNIPEKGFKASLGWCRRMMRRYDLSLR
Retrocopy GPKNGRFALVDQRVAEYVRYMQAKGDPITREAMQLKALEIAQEMNIPEKGFKASLGWCRRMMRRYDLSLR

Parental  HKVPVPQHLPEDLTEKLITYQRTVLSLRRAHDYEVTQMGNADETPICLEVPSRVTVDNQGEKPVLVKTPG
          HKVPVPQHLPEDLTEKLITYQ.TVLSLRRAHDYEVTQMGNADETPICLEVPSRVTVDNQGEKPVLVKTPG
Retrocopy HKVPVPQHLPEDLTEKLITYQQTVLSLRRAHDYEVTQMGNADETPICLEVPSRVTVDNQGEKPVLVKTPG

Parental  REKLRITAMLGVLADGKKLPPYIILRGTYIPPGKFPSGMEIRCHRYGWMTEDLMQDWLEVVWRRRTGALP
          REKLRITAMLGVLADGKKLPPYIILRGTYIPPGKFPSGMEIRCH.YGWMTEDLMQDWLEVVW.RRTGALP
Retrocopy REKLRITAMLGVLADGKKLPPYIILRGTYIPPGKFPSGMEIRCHCYGWMTEDLMQDWLEVVWKRRTGALP

Parental  KQRGMLILNGFRGHATDSVKSSMESLNTDMVIIPGSLTPQLQVLDVVVYKPLNDSVRAQYSNWLLAGNLA
          KQRG.LILNGFRGHATDSVK.....LNTDMVIIPGSLTPQLQVLDVVVYKPLNDSVRAQY.NWLL.GNLA
Retrocopy KQRGVLILNGFRGHATDSVK----NLNTDMVIIPGSLTPQLQVLDVVVYKPLNDSVRAQYYNWLLVGNLA

Parental  LSPTGNAKKPPLGLFLEWVMVAWNSISSESIVQGFKKCHISSNLEEEDDELWEIE-SELPGGGEPPKECD
          LSPTGN.KK.PLGLFLEWVMVAWNSISSESIVQGF.KCHISSNLEEEDDELWEIE.SELPGGGEPPKECD
Retrocopy LSPTGNSKKSPLGLFLEWVMVAWNSISSESIVQGF-KCHISSNLEEEDDELWEIE<SELPGGGEPPKECD

Parental  TESMTEGN
          .ESMTEGN
Retrocopy IESMTEGN

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_612 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000033914	1 retrocopy	retro_cjac_2779,
Dipodomys ordii	ENSDORG00000006822	1 retrocopy	retro_dord_612 ,
Erinaceus europaeus	ENSEEUG00000014393	1 retrocopy	retro_eeur_21,
Latimeria chalumnae	ENSLACG00000014539	1 retrocopy	retro_lcha_56,
Mus musculus	ENSMUSG00000040596	1 retrocopy	retro_mmus_2572,
Otolemur garnettii	ENSOGAG00000007615	1 retrocopy	retro_ogar_2784,
Tarsius syrichta	ENSTSYG00000011078	1 retrocopy	retro_tsyr_1983,