RetrogeneDB ID: retro_itri_1301

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393431.1:4553445..4553847(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHCHD3
• Ensembl ID: ENSSTOG00000022282
• Aliases: None
• Description: coiled-coil-helix-coiled-coil-helix domain containing 3 [Source:HGNC Symbol;Acc:21906]

Sequence

>retro_itri_1301
CGAGAGAGAGATGCTGCCAATGAGCTGTTGACTACAACTTTTCTTTGGGGGAGGCTACCTCAGTGAAGAGCATGACTTTT
TGGCAAAGCACCTGGCTGAACAGCTGGAAGGAAAAGACCAAGTGATAAAGAGGCAGGATGCATTCTACAAAGAGTAACTG
GCTACAATGGAGAGAAGTATTCATAGTCCTAAAGAGTCACCACCAAGCAATAGCAGATGGCTACAGAAGAAGTGGAAGCA
AAGTTCAAGCAAGATGAATTTTATCTAGTTTGTGCTGATTTCCCACTGAAAATTGTCCCGTGTTACCACAAGCATACCTA
CCCGAACATCAGCTGCTCTGCTCCAATCGGCCATAATATACACTCTGTCAATCATCTCCAACAGAACCTGATTGAGCAGG
GA

Alignment

ORF - retro_itri_1301 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.74 %
• Parental protein coverage: 59.03 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RERADANEQLTRAILRERIS-SEEERAKAKHLVKQLEEKDRLIKKQDAFYKEQLARLE-ERSSEFYKVTT
          RER..ANE.LT...L..R...SEE....AKHL..QLE.KD..IK.QDAFYKE.LA..E.E..S....VTT
Retrocopy RERDAANELLTTTFLWGRLP>SEEHDFLAKHLAEQLEGKDQVIKRQDAFYKE*LATME<EKYS*S*RVTT

Parental  EQYQKAAEEVEAKFKRYEYHPVCADLQAQILQCYRQNSHQTLSCSALANQYMHCVNHAKQSMLEKG
          .Q.Q.A.EEVEAKFK..E...VCAD....I..CY........SCSA......H.VNH..Q...E.G
Retrocopy KQ*QMATEEVEAKFKQDEFYLVCADFPLKIVPCYHKHTYPNISCSAPIGHNIHSVNHLQQNLIEQG

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_1301 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1301 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 12 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001312	1 retrocopy	retro_cfam_374,
Dasypus novemcinctus	ENSDNOG00000004942	1 retrocopy	retro_dnov_2559,
Homo sapiens	ENSG00000106554	3 retrocopies	retro_hsap_358, retro_hsap_3759, retro_hsap_542,
Macaca mulatta	ENSMMUG00000001671	1 retrocopy	retro_mmul_14,
Mus musculus	ENSMUSG00000053768	1 retrocopy	retro_mmus_3452,
Nomascus leucogenys	ENSNLEG00000012967	3 retrocopies	retro_nleu_168, retro_nleu_716, retro_nleu_904,
Oryctolagus cuniculus	ENSOCUG00000014032	1 retrocopy	retro_ocun_801,
Pongo abelii	ENSPPYG00000025827	5 retrocopies	retro_pabe_2492, retro_pabe_3161, retro_pabe_345, retro_pabe_411, retro_pabe_501,
Pan troglodytes	ENSPTRG00000019711	4 retrocopies	retro_ptro_2550, retro_ptro_282, retro_ptro_407, retro_ptro_701,
Rattus norvegicus	ENSRNOG00000013211	1 retrocopy	retro_rnor_2874,
Sorex araneus	ENSSARG00000012111	1 retrocopy	retro_sara_592,
Ictidomys tridecemlineatus	ENSSTOG00000022282	1 retrocopy	retro_itri_1301 ,