RetrogeneDB ID: retro_dord_293

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_102597:440..986(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mtfr1
• Ensembl ID: ENSDORG00000016322
• Aliases: None
• Description: mitochondrial fission regulator 1 [Source:MGI Symbol;Acc:MGI:1914722]

Sequence

>retro_dord_293
ATGCTTAGCTGAATTAAGTGCCTGATGAGGATGGTTTTGCAACAAGTTGGAATAAGCATGCAATCGGTACTTTGGTCTGG
AAAGCCATATGGTTCATCTTGAAGTATCGTAAGGAAAATTGGTACTAACTTATCTCTGATTCAGTGTCCAAGAGTTCAGT
TTCAGCTTACCAGCCATGAGACAAAATGGAGTCCCAAACACCCAGATGAGGATGCAGTGGCATCTTTTGCTGATGTTGGA
TGGGTGGCCACAGAAGAAGGAGAGTGCTCAACAAGACTAAGGACAGAAGTCACGTCAAAACCACCCCATCAGGACTGCCT
TCCTTACCTTGAGAAGTCCCCAAGCAGGCAGATTTCTTTACCAAACTTGTCTCAAGAAGATCTTCCACTGAAGACTGCAG
CACTGGCCAATGAGGAAGCACTGCAGAAGATCTCTGCACTTGAAAATGAGCTTGCTGCTCTGCGAGCTCAGATTGCCAAA
ATTGTAACCCTGCAAGAGCAGCAAAATCTCGTTACAGGTGACTTAGAATCTACCACATCTGTTACC

Alignment

ORF - retro_dord_293 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.56 %
• Parental protein coverage: 54.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLSWIKCLMRMVLQQVGISMQSVLWSGKPYGSSRSIVRKIGTNXXXXXXXXXXXXLTSHETEWSPKHPDE
          MLS.IKCLMRMVLQQVGISMQSVLWSGKPYGSS.SIVRKIGTN............LTSHET.WSPKHPDE
Retrocopy MLS*IKCLMRMVLQQVGISMQSVLWSGKPYGSS*SIVRKIGTNLSLIQCPRVQFQLTSHETKWSPKHPDE

Parental  DAVASFADVGWVATEEGECSTRLRTEVTSKPPHQDCLPYLEKSPSRQVSLPNLSQEDPPLKTAALANEEA
          DAVASFADVGWVATEEGECSTRLRTEVTSKPPHQDCLPYLEKSPSRQ.SLPNLSQED.PLKTAALANEEA
Retrocopy DAVASFADVGWVATEEGECSTRLRTEVTSKPPHQDCLPYLEKSPSRQISLPNLSQEDLPLKTAALANEEA

Parental  LQKISALENELAALRAQIAKIVTLQEQQNLVTGDLDSTTSST
          LQKISALENELAALRAQIAKIVTLQEQQNLVTGDL.STTS.T
Retrocopy LQKISALENELAALRAQIAKIVTLQEQQNLVTGDLESTTSVT

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_293 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 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012281	1 retrocopy	retro_amel_1640,
Choloepus hoffmanni	ENSCHOG00000006664	3 retrocopies	retro_chof_1268, retro_chof_2700, retro_chof_483,
Dipodomys ordii	ENSDORG00000016322	1 retrocopy	retro_dord_293 ,
Homo sapiens	ENSG00000066855	1 retrocopy	retro_hsap_4849,
Macaca mulatta	ENSMMUG00000011263	1 retrocopy	retro_mmul_2590,
Mustela putorius furo	ENSMPUG00000009909	2 retrocopies	retro_mputfur_1244, retro_mputfur_894,
Oryctolagus cuniculus	ENSOCUG00000008165	1 retrocopy	retro_ocun_1594,
Pongo abelii	ENSPPYG00000018631	1 retrocopy	retro_pabe_3769,
Rattus norvegicus	ENSRNOG00000021359	1 retrocopy	retro_rnor_1821,
Tarsius syrichta	ENSTSYG00000010102	1 retrocopy	retro_tsyr_1899,