RetrogeneDB ID: retro_itri_886

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393338.1:900828..901697(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EEF1G
• Ensembl ID: ENSSTOG00000002851
• Aliases: None
• Description: eukaryotic translation elongation factor 1 gamma [Source:HGNC Symbol;Acc:3213]

Sequence

>retro_itri_886
AAGTCGAGGACTTTTCTTGTGGACGAACGAGTGACACTGGCTGACATCACAGTTGTCTGCACCCTGTTGTGGCTCTATAA
ACAGGTCTTGGAACCTTCTTTTTGCCAGGCCTTTCCCAATACCAATCGCTGGTTCCTTACCTGCATTAACCAGCCCCAGT
TCCGGGCTATCTTGGGTGAGGTGAAACTGTGTGAGAAGATGGCTCAGTTTGATGCTAAGAAGTTTGCAGAGAGCCAGCCT
AAAAAGGACACCCCTCGGAAAGAAAAGGGTTCGCGGGAAGAGAAGCAGAAGCCCCAGGCAGAGCAGAAGAAAAAAAGGCA
GCTGCCTCAGCTCCAGAGGAGGAGATGGATGAATGTGAGCAGGCACTGGCTGCTGAGCCCAAGGCCAAGGACCCCTTTGC
TCACCTGCCTAAGAGTACCTTTGTGTTGGATGAATTTAAACTCAAATACTCCAATGAGGACATGCTCTCTGTGGCCCTGT
CATATCTTTGGGAGCACTTTGATAAGGATGGTTGGTCCTTGTGGTACGCTGAGTACCGCTTTCCTGAAGAGCTCACCCAG
ACCTTCATGAGTTGCAGTCTCATTACTGGAATGTTTCAGTGATTGGACAAGCTGAGGAAGAACGCCTTTGCCAGTGTCAT
CCTCTTTGGAACCAACAATAGCAGCTCCATTTCTGGAGTCTGGGTCTTCCGAGGCCAGGCGCTTGCCTTTCCGCTGAGTC
CAGATTGGCAGGTGGACCATGAATCATACACATGTCGAAAACTAGATCCTGGCAGCGAGGAGACCCAGACCCTGGTTCGA
GAGTACTTTTCCTGGGAAGGGGCCTTCCAGCATGTGGGCAAAGCCTTCAATCAGGGCAAGATCTTCAAG

Alignment

ORF - retro_itri_886 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.07 %
• Parental protein coverage: 66.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KTRTFLVGERVTLADITVVCTLLWLYKQVLEPSFRQAFPNTNRWFLTCINQPQFRAILGEVKLCEKMAQF
          K.RTFLV.ERVTLADITVVCTLLWLYKQVLEPSF.QAFPNTNRWFLTCINQPQFRAILGEVKLCEKMAQF
Retrocopy KSRTFLVDERVTLADITVVCTLLWLYKQVLEPSFCQAFPNTNRWFLTCINQPQFRAILGEVKLCEKMAQF

Parental  DAKKFAESQPKKDT-PRKEKGSREEKQKPQAERKEEKKAAASAPEEEMDECEQALAAEPKAKDPFAHLPK
          DAKKFAESQPKKDT.P...KG...........R.EEKKAAASAPEEEMDECEQALAAEPKAKDPFAHLPK
Retrocopy DAKKFAESQPKKDT<PSERKGFAGREAEAPG-RAEEKKAAASAPEEEMDECEQALAAEPKAKDPFAHLPK

Parental  STFVLDEFKRKYSNEDTLSVALPYFWDHFDKDGWSLWYAEYRFPEELTQTFMSCNLITGMFQRLDKLRKN
          STFVLDEFK.KYSNED.LSVAL.Y.W.HFDKDGWSLWYAEYRFPEELTQTFMSC.LITGMFQ.LDKLRKN
Retrocopy STFVLDEFKLKYSNEDMLSVALSYLWEHFDKDGWSLWYAEYRFPEELTQTFMSCSLITGMFQ*LDKLRKN

Parental  AFASVILFGTNNSSSISGVWVFRGQELAFPLSPDWQVDYESYTWRKLDPGSEETQTLVREYFSWEGAFQH
          AFASVILFGTNNSSSISGVWVFRGQ.LAFPLSPDWQVD.ESYT.RKLDPGSEETQTLVREYFSWEGAFQH
Retrocopy AFASVILFGTNNSSSISGVWVFRGQALAFPLSPDWQVDHESYTCRKLDPGSEETQTLVREYFSWEGAFQH

Parental  VGKAFNQGKIFK
          VGKAFNQGKIFK
Retrocopy VGKAFNQGKIFK

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_886 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_886 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 13 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015834	6 retrocopies	retro_cfam_1241, retro_cfam_1398, retro_cfam_1862, retro_cfam_478, retro_cfam_638, retro_cfam_653,
Erinaceus europaeus	ENSEEUG00000001231	1 retrocopy	retro_eeur_575,
Homo sapiens	ENSG00000254772	4 retrocopies	retro_hsap_2778, retro_hsap_2982, retro_hsap_3906, retro_hsap_4744,
Gorilla gorilla	ENSGGOG00000013557	12 retrocopies	retro_ggor_1935, retro_ggor_1936, retro_ggor_1991, retro_ggor_1992, retro_ggor_2064, retro_ggor_2065, retro_ggor_2214, retro_ggor_243, retro_ggor_2542, retro_ggor_2633, retro_ggor_2946, retro_ggor_2947,
Latimeria chalumnae	ENSLACG00000014700	1 retrocopy	retro_lcha_82,
Loxodonta africana	ENSLAFG00000003339	1 retrocopy	retro_lafr_381,
Macaca mulatta	ENSMMUG00000006598	5 retrocopies	retro_mmul_1447, retro_mmul_1905, retro_mmul_2528, retro_mmul_736, retro_mmul_802,
Monodelphis domestica	ENSMODG00000007691	1 retrocopy	retro_mdom_68,
Mus musculus	ENSMUSG00000071644	7 retrocopies	retro_mmus_1447, retro_mmus_1839, retro_mmus_2350, retro_mmus_2765, retro_mmus_3080, retro_mmus_425, retro_mmus_989,
Nomascus leucogenys	ENSNLEG00000003528	2 retrocopies	retro_nleu_1510, retro_nleu_681,
Pan troglodytes	ENSPTRG00000003768	3 retrocopies	retro_ptro_1879, retro_ptro_2017, retro_ptro_3159,
Rattus norvegicus	ENSRNOG00000020075	8 retrocopies	retro_rnor_1312, retro_rnor_2126, retro_rnor_2235, retro_rnor_2269, retro_rnor_2468, retro_rnor_2617, retro_rnor_2928, retro_rnor_979,
Ictidomys tridecemlineatus	ENSSTOG00000002851	2 retrocopies	retro_itri_852, retro_itri_886 ,