RetrogeneDB ID: retro_dord_133

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_3716:325032..325485(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Zmat2
• Ensembl ID: ENSDORG00000014559
• Aliases: None
• Description: zinc finger, matrin type 2 [Source:MGI Symbol;Acc:MGI:1913742]

Sequence

>retro_dord_133
AAAACCAGCGAGCCAGTCAAGAGGGAGTTTCAGTAACACAGAGACTATAAAGTGGGCTCATCTTCCCAAGATTGGATTCC
AAATGTCATGACCAAGACAACCCCACCATCTGAGATGGGAGGATATTACTGCAGTGTCTATGACTGTGTGAGAGTCTCCA
TCAACTTCCTGGATCATATGAATGGAAAGAATCAACAGAACCTGGGCATGCCTAGGGATGTGGAACGTTCTATCCTGGAT
CAGGTGAAGAAAGGCTTTTGAGGTCGGTCAATAAGACGTAAACCAGCTGAAGGATTATGATTCTGAGCAAAGGATGAAGA
AACTCAGAGGAAGAAAAGGCTAAAGCATACAAGAATGAAAAGAACAGGAGAGTGAAGGAGGACTTGACATTTGAGGAGGT
GGAGATGGCGGCTGTGATGGCTTCTTGGCTGTGGTTCCACCAAGAAGAGTTTC

Alignment

ORF - retro_dord_133 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.21 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KPVQPVKRELLRHRDYKVDLESKLGKTIVITKTTPQSEMGGYYCNVCDCVVKDSINFLDHINGKKHQRNL
          K...PVKRE...HRDYKV...S......V.TKTTP.SEMGGYYC.V.DC.V..SINFLDH.NG.K.Q.NL
Retrocopy KTSEPVKREFQ*HRDYKVGSSSQDWIPNVMTKTTPPSEMGGYYCSVYDC-VRVSINFLDHMNG-KNQQNL

Parental  GMSMRVERSTLDQVK-KRFEVNKKKMEEKQKDYDFEERMKELR-EEEEKAKAYKKEKQKEKKRRAEEDLT
          GM...VERS.LDQVK.K.FEV..........DYD.E.RMK.LR.EE..KAKAYK.EK......R..EDLT
Retrocopy GMPRDVERSILDQVK>KAFEVGQ*DVNQLK-DYDSEQRMKKLR>EE--KAKAYKNEKNR----RVKEDLT

Parental  FEEDDEMAAVM-GF-SGFGSTKKSY
          FEE..EMAAVM.GF..G.GSTKKS.
Retrocopy FEE-VEMAAVM<GF<LGCGSTKKSF

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_133 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 11 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005907	1 retrocopy	retro_cfam_822,
Choloepus hoffmanni	ENSCHOG00000007795	2 retrocopies	retro_chof_101, retro_chof_514,
Callithrix jacchus	ENSCJAG00000016231	3 retrocopies	retro_cjac_1137, retro_cjac_1472, retro_cjac_4007,
Dipodomys ordii	ENSDORG00000014559	8 retrocopies	retro_dord_123, retro_dord_127, retro_dord_129, retro_dord_131, retro_dord_133 , retro_dord_135, retro_dord_136, retro_dord_138,
Echinops telfairi	ENSETEG00000005406	2 retrocopies	retro_etel_156, retro_etel_882,
Ficedula albicollis	ENSFALG00000008988	1 retrocopy	retro_falb_9,
Myotis lucifugus	ENSMLUG00000017525	2 retrocopies	retro_mluc_2281, retro_mluc_2309,
Monodelphis domestica	ENSMODG00000011269	1 retrocopy	retro_mdom_1209,
Pteropus vampyrus	ENSPVAG00000009717	1 retrocopy	retro_pvam_827,
Ictidomys tridecemlineatus	ENSSTOG00000002025	1 retrocopy	retro_itri_1272,
Tursiops truncatus	ENSTTRG00000001777	4 retrocopies	retro_ttru_1889, retro_ttru_340, retro_ttru_721, retro_ttru_766,