RetrogeneDB ID: retro_dord_495

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_23496:19241..19726(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Anp32e
• Ensembl ID: ENSDORG00000011690
• Aliases: None
• Description: acidic (leucine-rich) nuclear phosphoprotein 32 family, member E [Source:MGI Symbol;Acc:MGI:1913721]

Sequence

>retro_dord_495
ATGGAGATGAAGAAGAGGATTAGTCTAGAGTTATGGAACAGAGTCCCAGAGGAGGTAACAGAGTTAGTCCTTGATAATTG
CCTGTGTATCAATGGGGAAATTGAAAGCCTGAATGACACTTTTAAGGAACTAGAGTTTCTGAGTATGGCTAATGTGAAAT
TAAGTTCACTGGCCTGGCTCCCTAGCTTGAATAAACTTTAAAGTTGGAACTTGGTGACAATATAATTTCTGTAGGTTTGG
AAGTCCTGGCAGAGAAATGTCCAAATCTTACTTACCTCAATCTGAGTGGAAACAAAATCAGAGATCTCAGTACTGTGGAA
GCTCTGAAAAATCTTAAAAATTTGAAAAGTCTTGACTAGTTCAACTGTGAGATCACAAACCTGGAAGATTACAGAGAAAG
TATTTTTGAGCTGTTGCAGCAAATCACATACTTAGATGGATTTGATCAGGAGGTTAAGGAAGCACCAGACTCGGAAGAGG
AAGAT

Alignment

ORF - retro_dord_495 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.73 %
• Parental protein coverage: 62.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEMH-RITLELRNKPXXXVTELVLDNCLCVNGEIEGLNDTFKELEFLSMANVKLSSLARLPSLNKL-RKL
          MEM..RI.LEL.N.....VTELVLDNCLC.NGEIE.LNDTFKELEFLSMANVKLSSLA.LPSLNKL..KL
Retrocopy MEMKKRISLELWNRVPEEVTELVLDNCLCINGEIESLNDTFKELEFLSMANVKLSSLAWLPSLNKL<LKL

Parental  ELGDNIISGGLEVLAEKCPNLTYLNLSGNKIKDLSTVEALQNLKNLKSLDLFNCEITNLEDYRESIFELL
          ELGDNIIS.GLEVLAEKCPNLTYLNLSGNKI.DLSTVEAL.NLKNLKSLD.FNCEITNLEDYRESIFELL
Retrocopy ELGDNIISVGLEVLAEKCPNLTYLNLSGNKIRDLSTVEALKNLKNLKSLD*FNCEITNLEDYRESIFELL

Parental  QQITYLDGFDQEDNEAPDSEEED
          QQITYLDGFDQE..EAPDSEEED
Retrocopy QQITYLDGFDQEVKEAPDSEEED

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_495 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 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009710	1 retrocopy	retro_cjac_2926,
Dipodomys ordii	ENSDORG00000008611	1 retrocopy	retro_dord_240,
Dipodomys ordii	ENSDORG00000011690	4 retrocopies	retro_dord_311, retro_dord_358, retro_dord_495 , retro_dord_777,
Loxodonta africana	ENSLAFG00000026778	1 retrocopy	retro_lafr_580,
Microcebus murinus	ENSMICG00000015265	1 retrocopy	retro_mmur_115,
Monodelphis domestica	ENSMODG00000027412	2 retrocopies	retro_mdom_1802, retro_mdom_569,
Ochotona princeps	ENSOPRG00000010058	3 retrocopies	retro_opri_1223, retro_opri_52, retro_opri_774,
Ictidomys tridecemlineatus	ENSSTOG00000004170	5 retrocopies	retro_itri_1003, retro_itri_1031, retro_itri_1359, retro_itri_394, retro_itri_955,
Tupaia belangeri	ENSTBEG00000001989	1 retrocopy	retro_tbel_918,