RetrogeneDB ID: retro_dord_558

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_32227:318..877(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Oaz1
• Ensembl ID: ENSDORG00000016529
• Aliases: None
• Description: ornithine decarboxylase antizyme 1 [Source:MGI Symbol;Acc:MGI:109433]

Sequence

>retro_dord_558
ATGGTGAAATCCTTGCTGCAGCAGATCCTCAACAACCACTGCTTCCTCTGAGAAAAGGAAGGGCATAAACCTAGCGCCAC
TATTCACACCAGCCACACCATGTTGCTCCTCACCCTGCAGAGCCATGGCAGCCAAAGCAGTGAGAGTTCCAGGGTCTCTC
TCAATTGCTATAGTAACCTGGGCTCCTGGTGCTCCTCATGTCCCTCACTCACCCCTAAAGATCCCAGGTGGACAAGGGAA
TAGTCAGAGGGATCACAATCTTTCAGTAACTTTTTCCCTCTGCTATGCAGCTGAATGTAACAGAGGAACTATGGTCTAAT
AACAAAACAAGAGTTCTCGGCATCTAGTCCAGGCTCACCAAGGCCAAACACAACACCTGGATAGCAGTATGAAGTCACAG
AAGTCTCTACATTGATCTCCCAGGAGGCCCTCTGCCTGAAGGGAGCAAGGAGGGTTTTGTAGTTCTACTGGAGTTTGCTG
AAAGAGATACTCTGAGATGTCTGTCTTCCTTTGCTCCCATAAGATCTGTGGGGGCAAAGCTGCCTTGCTTCCCTCCTTC

Alignment

ORF - retro_dord_558 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.32 %
• Parental protein coverage: 83.63 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MVKSSLQRILNSHCFAREKEGDKPSATVHTSRIMPLLSLHSRGGRSSESSRVSLNCCSNLG-PGPQWCDV
          MVKS.LQ.ILN.HCF..EKEG.KPSAT.HTS..M.LL.L.S.G..SSESSRVSLNC.SNLG.PG.....V
Retrocopy MVKSLLQQILNNHCFL*EKEGHKPSATIHTSHTMLLLTLQSHGSQSSESSRVSLNCYSNLG>PGAP--HV

Parental  PHPPLKIPGGRGNSQRDHNLS-ANLF-YSDNRLNVTEELTSNNKTRILSVQSRLTEAKHITWRAVWSGSS
          PH.PLKIPGG.GNSQRDHNLS..N.F..S...LNVTEEL.SNNKTR.L...SRLT.AKH.TW.AV.S..S
Retrocopy PHSPLKIPGGQGNSQRDHNLS<SNFF<PSAMQLNVTEELWSNNKTRVLGI*SRLTKAKHNTWIAV*SHRS

Parental  LYIELPGGPLPEGSKDSFAVLLEFAE-EQLRADHVFICFHKNREDRAALFRTF
          LYI.LPGGPLPEGSK..F.VLLEFAE........VF.C.HK.....AAL...F
Retrocopy LYIDLPGGPLPEGSKEGFVVLLEFAE<KRYSEMSVFLCSHKICGGKAALLPSF

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_558 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000016529	2 retrocopies	retro_dord_558 , retro_dord_654,
Echinops telfairi	ENSETEG00000017945	2 retrocopies	retro_etel_2073, retro_etel_452,
Myotis lucifugus	ENSMLUG00000004446	2 retrocopies	retro_mluc_1524, retro_mluc_2157,
Mus musculus	ENSMUSG00000035242	1 retrocopy	retro_mmus_1622,
Nomascus leucogenys	ENSNLEG00000002179	1 retrocopy	retro_nleu_2435,
Pongo abelii	ENSPPYG00000009345	1 retrocopy	retro_pabe_476,