RetrogeneDB ID: retro_dord_141

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_372:68219..68790(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Txndc9
• Ensembl ID: ENSDORG00000013557
• Aliases: None
• Description: thioredoxin domain containing 9 [Source:MGI Symbol;Acc:MGI:2138153]

Sequence

>retro_dord_141
TCTGTCCTCATGTTTTCAAAAGCCCTGAAAAACCAGTTGCTTCAGACGACCAAGCTGGTAGAAGAAATTAAGAAACTGCA
CCTGGTGGATGAAGATGAATTGGAGCACAACAAAGAAAAGAGACTTGAGGCACTAAGGAAAGTTCAGCAGCAGAAACAGG
AATGGCTTTCTAAAGGACATGGTGAATGCAGAGAAATACCTAGTGAGAAAGACTCTTTTCCAATAAGTCAAAGAGAGTAA
AAAGTAGTTTGCCATTTCTATAAAGTATAGTACCCTACATTCAGGTACAAAATCCTAGACAGACATTTGGTGATACTAAG
AAACATCTTGAGACCAAAGTTTTGAAGCTGAATGTCGAAAAAGCACCTTTTCTTTGTGAGAGACTACATACTAAACTCAT
TCTCACACTAGCACTGGTAAAAGAGGGGAAAACACAAGATTATGTTTTTGGATTTACCAACCTAGAAATACAGATGATGA
TTTCACCACAGAAACTTTAGAACGGAGGCTCAGCTGTTCTGATATTCTTAATTACAGTGGAAATTTAATGGGGCCACCAT
TCAGAGCTAAA

Alignment

ORF - retro_dord_141 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.37 %
• Parental protein coverage: 83.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SKVLENQLLQTTKLVEDHLDSEIKKLDQMDEDELERLKEKRLAALRKAQQQKQEWLSKGHGEYREIPSER
          S.......L....L....L..EIKKL...DEDELE..KEKRL.ALRK.QQQKQEWLSKGHGE.REIPSE.
Retrocopy SVLMFSKALKNQLLQTTKLVEEIKKLHLVDEDELEHNKEKRLEALRKVQQQKQEWLSKGHGECREIPSEK

Parental  D-FFQEVKESK-KVVCHFYR--DSTFRCKILDRHLVILSKKHLETKF-LKLNVDKAPFLCERLRIKVLPT
          D..FQ.VKESK.KVVCHFY.....TFR.KILDRHLVIL....L..KF.LKLNV.KAPFLCERL..K...T
Retrocopy D>LFQ*VKESK<KVVCHFYKV*YPTFRYKILDRHLVIL-RNILRPKF<LKLNVEKAPFLCERLHTKLILT

Parental  LALIKDGKTQDYVVGFTDL-GNT-DDFTTETLEWRLGCSDILNYSGNLMEPPFQSQ
          LAL.K.GKTQDYV.GFT.L..NT.DDFTTETLE.RL.CSDILNYSGNLM.PPF...
Retrocopy LALVKEGKTQDYVFGFTNL<RNTDDDFTTETLERRLSCSDILNYSGNLMGPPFRAK

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_141 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009936	1 retrocopy	retro_cjac_500,
Dipodomys ordii	ENSDORG00000013557	1 retrocopy	retro_dord_141 ,
Homo sapiens	ENSG00000115514	1 retrocopy	retro_hsap_3042,
Gorilla gorilla	ENSGGOG00000024615	1 retrocopy	retro_ggor_2096,
Myotis lucifugus	ENSMLUG00000008110	1 retrocopy	retro_mluc_717,
Mus musculus	ENSMUSG00000058407	2 retrocopies	retro_mmus_2791, retro_mmus_873,
Pan troglodytes	ENSPTRG00000012278	1 retrocopy	retro_ptro_1996,