RetrogeneDB ID: retro_dord_649

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_47799:7075..7483(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Hnrnpd
• Ensembl ID: ENSDORG00000012507
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein D [Source:MGI Symbol;Acc:MGI:101947]

Sequence

>retro_dord_649
GTCATGGATCAGAAAGAACATAAATTGAACGGGAAAGTGATTGATCCTAACAGGGCCAAAGCCATGAAAACAAAAAAGTC
CGTCATAAAAATTTGTATTGGTGGCCTTTCTCCAGATACAGCTGAAGAGAAAATAAGGGAGTACTTTGGTGGCTTTGGTG
AGGTGGAATCAATAGAGCTCACCATGGGCAACAAGACCAATAAGTGTGGGTTCTGCTTGATTACTTTTAAAGAAGAACCA
GTGAAGAAGATAATGGAAAAAAATACCACAATGTCGGTCTTAGTAAATGTGAAATAGAAGTAGCCATGTCGAAGAACAGT
ATCAGCAACAGCAGCAGTGGGGGTCTAGAGGAGGATTTGCAGGACCAGCTGTGGAAGAGGTGGTGACCAGCAGAGTGGTT
ATGGGAAA

Alignment

ORF - retro_dord_649 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.28 %
• Parental protein coverage: 53.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VMDQKEHKLNGKVIDPKRAKAMKTKEPVKKIFVGGLSPDTPEEKIREYFGGFGEV-SIELPMDNKTNKRR
          VMDQKEHKLNGKVIDP.RAKAMKTK..V.KI..GGLSPDT.EEKIREYFGGFGEV.SIEL.M.NKTNK..
Retrocopy VMDQKEHKLNGKVIDPNRAKAMKTKKSVIKICIGGLSPDTAEEKIREYFGGFGEVESIELTMGNKTNK-C

Parental  GFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVAMSK-EQYQQQQQWGSRGGFAGRA-RGRGGGPSQNW
          GFC.ITFK.EEPVKKIME.KKYHNVGLSKCEI.VAMSK.EQYQQQQQWGSRGGFAG.A..GRGG......
Retrocopy GFCLITFK-EEPVKKIME<KKYHNVGLSKCEIEVAMSK<EQYQQQQQWGSRGGFAGPA<CGRGGDQQSGY

Parental  NQ
          ..
Retrocopy GK

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_649 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015165	1 retrocopy	retro_cjac_2796,
Dipodomys ordii	ENSDORG00000000968	1 retrocopy	retro_dord_145,
Dipodomys ordii	ENSDORG00000005482	1 retrocopy	retro_dord_489,
Dipodomys ordii	ENSDORG00000012507	1 retrocopy	retro_dord_649 ,
Homo sapiens	ENSG00000138668	1 retrocopy	retro_hsap_4689,
Gorilla gorilla	ENSGGOG00000026760	1 retrocopy	retro_ggor_2916,
Loxodonta africana	ENSLAFG00000016483	1 retrocopy	retro_lafr_686,
Pan troglodytes	ENSPTRG00000016215	1 retrocopy	retro_ptro_3116,
Sarcophilus harrisii	ENSSHAG00000013312	1 retrocopy	retro_shar_752,
Tarsius syrichta	ENSTSYG00000010395	3 retrocopies	retro_tsyr_1092, retro_tsyr_2070, retro_tsyr_269,
Tursiops truncatus	ENSTTRG00000007592	1 retrocopy	retro_ttru_1913,
Vicugna pacos	ENSVPAG00000004374	2 retrocopies	retro_vpac_484, retro_vpac_97,