RetrogeneDB ID: retro_itri_1003

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393358.1:34603..35048(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000006079
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ANP32E
• Ensembl ID: ENSSTOG00000004170
• Aliases: None
• Description: acidic (leucine-rich) nuclear phosphoprotein 32 family, member E [Source:HGNC Symbol;Acc:16673]

Sequence

>retro_itri_1003
TTAAGGAACCGAGCCCCGGAGGAGGTGACACACTTAGTTCTTGATAATTGCCTGTGTGTCAATGGGGAAATTGAAGGCCT
GAATGACACTTTTAAAGAACTAGAGTTTCTGAGTATGGCTAATGTGGAATTAGATTCACTGGCCCAACTTCCCAGCTTAA
ACAAACTTCGAAAGTTGGAACTTAGTGACACTATAATTTCTGGAGGCTTGGAAGTCCTGGCAGAAAAATGTCCAAATCTT
ACCTACCTCAATCTGAGTAGAAACAAAATCAAAGATCTTATTTAGTACAGTAGAAGCTCTGCAAAATCTTAAAAATTTGA
AAAGTCTTGACTTGTTTAACGGTGAGATCACAAATCTGGAAGATTACAGAGAAAGTATTTTTGAATTGCTGCAACAAATC
ACATACTTAGATGGATTTGATCAGGAGGAGAATGAAGCACCTAAC

Alignment

ORF - retro_itri_1003 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.93 %
• Parental protein coverage: 61.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LRNRVSNQVTELVLDNCLCVNGEIEGLNDTFKELEFLSMANVELSSLAQLPSLNKLRKLELSDNIISGGL
          LRNR....VT.LVLDNCLCVNGEIEGLNDTFKELEFLSMANVEL.SLAQLPSLNKLRKLELSD.IISGGL
Retrocopy LRNRAPEEVTHLVLDNCLCVNGEIEGLNDTFKELEFLSMANVELDSLAQLPSLNKLRKLELSDTIISGGL

Parental  EVLAEKCPNLTYLNLSGN-KIKDL-STVEALQNLKNLKSLDLFNCEITNLEDYRESIFELLQQITYLDGF
          EVLAEKCPNLTYLNLS.N.K.K.L.STVEALQNLKNLKSLDLFN.EITNLEDYRESIFELLQQITYLDGF
Retrocopy EVLAEKCPNLTYLNLSRN>KSKILFSTVEALQNLKNLKSLDLFNGEITNLEDYRESIFELLQQITYLDGF

Parental  DQEDNEAPD
          DQE.NEAP.
Retrocopy DQEENEAPN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1003 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1003 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009710	1 retrocopy	retro_cjac_2926,
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,
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,