RetrogeneDB ID: retro_dord_299

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_10640:30264..30957(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDORG00000006945
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Fhl1
• Ensembl ID: ENSDORG00000015644
• Aliases: None
• Description: four and a half LIM domains 1 [Source:MGI Symbol;Acc:MGI:1298387]

Sequence

>retro_dord_299
ATGGATGACAAGTACCACTGCCACCACTGCAAGGAATCCTTGCAGGGGAAGAAGTATGTGGAGAAGGAAAACCAGTCGTA
CTGCGTGAAGTGCTTCGACAAGTTCTGTGCCAACACCTGCGTGGAATGCCACCTGCCCATCGGCGCGGACTCTAAGGAAG
TGCACTACAAGGGCCACTTTTGGCACGACACCTGCTTCCGTTGTTCCAAGTGTTCGCACACCTTGGCCTCGGAGAGCTTT
ATGGCCAAGGACAACAAGATCCTGTGCAACAACTGTGCCGCTAGTACCGAGGAATCCCCCAAGTGCAAAGGGTGCTCCAA
GTCCTTCGTGGCCGGAGACCAGAACGTGGAGTACAAGGGCGCTTACTGGCACAAAGACTGCTTCCTCTGCAGCAACTGCA
AGAAAATCATCGGCACCGACAGCTTCTTCGCGAAAGGGGAAGAGATGTACTGCGCCGCTTGTCATGCGGCCAAGTTTTCC
AAGCAGTGCGTCAAGTGCGCAAAGCCCATCACATCGGGAGGAATCACGTACCAGAACCAGCCCTGGCATGCTGATTGCTT
TGTGTGCGTTTCCTGCTCCAAGAAGCTGGCTGAGCAGCATTTCACGGCCGTGGAGGATAAGTATTACTGCGTGGAGTGCT
ACAAGAACTTTGTGGCCAAGAAGTGTGCGGGATGCCGTAACCCCATCACTGGG

Alignment

ORF - retro_dord_299 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.46 %
• Parental protein coverage: 71.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEKFDCHYCRDPLQGKKYVEKDGHHCCLKCFDKFCANTCVECRKPIGADSKEVHYKNRFWHDSCFRCAK
          M..K..CH.C...LQGKKYVEK.....C.KCFDKFCANTCVEC..PIGADSKEVHYK..FWHD.CFRC.K
Retrocopy MDDKYHCHHCKESLQGKKYVEKENQSYCVKCFDKFCANTCVECHLPIGADSKEVHYKGHFWHDTCFRCSK

Parental  CFHPLANETFVAKDNKILCNKCATRGEDNPRCKGCFKALVAGDQNVEYKGLVWHKDCFTCSNCKQVIGTG
          C.H.LA.E.F.AKDNKILCN.CA...E..P.CKGC.K..VAGDQNVEYKG..WHKDCF.CSNCK..IGT.
Retrocopy CSHTLASESFMAKDNKILCNNCAASTEESPKCKGCSKSFVAGDQNVEYKGAYWHKDCFLCSNCKKIIGTD

Parental  SFFPKGEDFYCVTCHETKFAKHCVKCNKAITSGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYC
          SFF.KGE..YC..CH..KF.K.CVKC.K.ITSGGITYQ.QPWHADCFVCV.CSKKLA.Q.FTAVED.YYC
Retrocopy SFFAKGEEMYCAACHAAKFSKQCVKCAKPITSGGITYQNQPWHADCFVCVSCSKKLAEQHFTAVEDKYYC

Parental  VDCYKNFVAKKCAGCKNPITG
          V.CYKNFVAKKCAGC.NPITG
Retrocopy VECYKNFVAKKCAGCRNPITG

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_299 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000015644	2 retrocopies	retro_dord_299 , retro_dord_722,
Homo sapiens	ENSG00000022267	1 retrocopy	retro_hsap_2878,
Gorilla gorilla	ENSGGOG00000010054	1 retrocopy	retro_ggor_1994,
Microcebus murinus	ENSMICG00000009342	1 retrocopy	retro_mmur_1438,
Myotis lucifugus	ENSMLUG00000014336	2 retrocopies	retro_mluc_311, retro_mluc_814,
Macaca mulatta	ENSMMUG00000007922	1 retrocopy	retro_mmul_1458,
Mus musculus	ENSMUSG00000023092	1 retrocopy	retro_mmus_51,
Pongo abelii	ENSPPYG00000020761	1 retrocopy	retro_pabe_2382,