RetrogeneDB ID: retro_dord_554

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_31539:2870..3923(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Fam118b
• Ensembl ID: ENSDORG00000016718
• Aliases: None
• Description: family with sequence similarity 118, member B [Source:MGI Symbol;Acc:MGI:1924483]

Sequence

>retro_dord_554
ATGGCTTCTACAGGGAGCCAGGCCTCTGATATAGACGAGATTTTTGGATTCTTCAGTGATGGCGAACCCCCCACCAAAAA
GCCCAGGAAGCTGCTTCCAAGCTTAAAAACTAAGAAGCCCCGAGAACTTGTGCTGGTGATTGGAACAGGCATCCGTGCTG
CAGTAGCACCTCAGGTTCCAGCCCTGAAATCCTGGAAGGGGTAAATTCAGGCTTTACTGGATGCTGCCATTGATTTTGAT
CTTCTAGAAGATGAGGAGAGCAAAAAGTTTCAGAAGTGTCTCCATGAAGATAAGAACCTTGTCCATGTTGCCCATGACCT
TATTCAGAAACTCTCTCCTTGTACCAGTAATGTTCGTTCTACATTTTTCAAAGACTGTTTATATGAAGTATTTGATGACC
TGGAGTCAAAGATAGAAGATTTTGGAAAACAGCTACTGCAGTCAGTTCTCCACTTGATGGAAAATGGGGCCCTAATACTA
ACTACAAATTTTGATAATCTCTTGGAACTGTATGCAGCAAACCACGGAAAACAGCTTGAGTCCCTTGACCTAACTGATGA
GAAAAAGGTTTTGGAGAGGGCTCAAGACAAGCACAAGCTGAGTGTGTTACACATCCATGGTGTCTACACCAACCCTATTG
GCATTGTCCTCCATCCATCTGGATATCAGAATGTGCTCATAAACACTGAAGTTATGAGAGAGATTCAGAAACTTTATGAA
AACAACTCTTTTCTTTTCCTGGGTTGTGGCTGGACTGTGGATGACACCACTTTCCAGGCCCTCTTCCTGGAGGCTGTCAA
GCATAAATCTGACTTAGAACATTTCATGCTGGTTCGGACAGGAAATGTTGATGAGTTCAAGAAACTTCGAGAAAACATGC
TGGATAAGGGGATTAAGGTCATCTCCTATGGAAATGACTACACTGATCTTCAAGAATATTTCAAGCGGCTGACAAGTGAG
ATTTCCACAAGGGGTAGATCAGCAGGGATGGTGAGAGAAGGCCAGCTAAATGGTTCATCTGCAGCACATAGTGAAATCAG
AGGCTGTAGTACA

Alignment

ORF - retro_dord_554 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.59 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASTGSQASDIDEIFGFFSDGEPPTKKPRKLLPSLKTKKPRELVLVIGTGISAAVAPQVPALKSWKGLIQ
          MASTGSQASDIDEIFGFFSDGEPPTKKPRKLLPSLKTKKPRELVLVIGTGI.AAVAPQVPALKSWKG.IQ
Retrocopy MASTGSQASDIDEIFGFFSDGEPPTKKPRKLLPSLKTKKPRELVLVIGTGIRAAVAPQVPALKSWKG*IQ

Parental  ALLDAAIDFDLLEDEESKKFQKCLHEDKNLVHVAHDLIQKLSPRTSNVRSTFFKDCLYEVFDDLESKMED
          ALLDAAIDFDLLEDEESKKFQKCLHEDKNLVHVAHDLIQKLSP.TSNVRSTFFKDCLYEVFDDLESK.ED
Retrocopy ALLDAAIDFDLLEDEESKKFQKCLHEDKNLVHVAHDLIQKLSPCTSNVRSTFFKDCLYEVFDDLESKIED

Parental  SGKQLLQSVLHLMENGALVLTTNFDNLLELYAADQGKQLESLDLTDEKKVLEWAQEKRKLSVLHIHGVYT
          .GKQLLQSVLHLMENGAL.LTTNFDNLLELYAA..GKQLESLDLTDEKKVLE.AQ.K.KLSVLHIHGVYT
Retrocopy FGKQLLQSVLHLMENGALILTTNFDNLLELYAANHGKQLESLDLTDEKKVLERAQDKHKLSVLHIHGVYT

Parental  NPSGIVLHPAGYQNVLRNTEVMREIQKLYENKSFLFLGCGWTVDDTTFQALFLEAVKHKSDLEHFMLVRR
          NP.GIVLHP.GYQNVL.NTEVMREIQKLYEN.SFLFLGCGWTVDDTTFQALFLEAVKHKSDLEHFMLVR.
Retrocopy NPIGIVLHPSGYQNVLINTEVMREIQKLYENNSFLFLGCGWTVDDTTFQALFLEAVKHKSDLEHFMLVRT

Parental  GDVDEFKKLRENMLDKGIKVISYGNDYADLPEYFKRLTSEISTRGRSAGMVREGQLNGSSAAHSEIRGCS
          G.VDEFKKLRENMLDKGIKVISYGNDY.DL.EYFKRLTSEISTRGRSAGMVREGQLNGSSAAHSEIRGCS
Retrocopy GNVDEFKKLRENMLDKGIKVISYGNDYTDLQEYFKRLTSEISTRGRSAGMVREGQLNGSSAAHSEIRGCS

Parental  T
          T
Retrocopy T

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_554 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000016718	1 retrocopy	retro_dord_554 ,
Erinaceus europaeus	ENSEEUG00000007898	1 retrocopy	retro_eeur_605,
Myotis lucifugus	ENSMLUG00000017329	1 retrocopy	retro_mluc_1535,
Oryctolagus cuniculus	ENSOCUG00000017049	1 retrocopy	retro_ocun_1272,
Otolemur garnettii	ENSOGAG00000008923	1 retrocopy	retro_ogar_1659,