RetrogeneDB ID: retro_itri_1138

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393384.1:3677053..3677455(+)
• Located in intron of: ENSSTOG00000010974

Retrocopy information

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

Parental gene information

• Parental gene symbol: NXT2
• Ensembl ID: ENSSTOG00000005243
• Aliases: None
• Description: nuclear transport factor 2-like export factor 2 [Source:HGNC Symbol;Acc:18151]

Sequence

>retro_itri_1138
CTACATGTAGCTCAGGCATGTAGAGCTACTGAGGAATTTGTCCATATTTACTATGAGACAATGGACAAAAGAAGAAGGAC
ACTTACCAGGCTGTATGTGGACAAGGCCACTTTAATATGGAATGGAAATGTTGTTACAGGGCTGGATGCCCTAAGTAATT
TTTTCAAGATGTTGCCTTCTAGTGAGTTCCAGATCAATATGTTAGATTGCCAACCAGACCATGTGCAAGCTACCCAGTCC
CAGACTATAGTTCTTGTTGTAACCAGTGGAACTATGAAGTTTGATGGAAACAAATAACATTTCTTCAACCAGAACTTCCT
GCTGACTGCTCCATCCGCTCCTAATAGCACTGTGTGGAAGATTGCTGGTTATTGCTTCTATTTCCAAGATTTGGCTAGTA
GT

Alignment

ORF - retro_itri_1138 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.58 %
• Parental protein coverage: 97.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MYVDQACRAAEEFVNIYYETMDKRRRALTRLYLDKATLIWNGNVVTGLDALSNFFEMLPSSEFQVNMLDC
          ..V.QACRA.EEFV.IYYETMDKRRR.LTRLY.DKATLIWNGNVVTGLDALSNFF.MLPSSEFQ.NMLDC
Retrocopy LHVAQACRATEEFVHIYYETMDKRRRTLTRLYVDKATLIWNGNVVTGLDALSNFFKMLPSSEFQINMLDC

Parental  QPVHEQATQSQTTVLVVTSGIVKFDGNKQHYFNQNFLLTAQSTPNSTVWKIASDCFRFQDWASS
          QP.H.QATQSQT.VLVVTSG..KFDGNK.H.FNQNFLLTA.S.PNSTVWKIA..CF.FQD.ASS
Retrocopy QPDHVQATQSQTIVLVVTSGTMKFDGNK*HFFNQNFLLTAPSAPNSTVWKIAGYCFYFQDLASS

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_1138 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1138 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 28 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017999	1 retrocopy	retro_amel_59,
Bos taurus	ENSBTAG00000020739	1 retrocopy	retro_btau_118,
Canis familiaris	ENSCAFG00000028574	1 retrocopy	retro_cfam_1137,
Callithrix jacchus	ENSCJAG00000007369	1 retrocopy	retro_cjac_98,
Cavia porcellus	ENSCPOG00000003310	1 retrocopy	retro_cpor_29,
Dipodomys ordii	ENSDORG00000010714	1 retrocopy	retro_dord_2,
Echinops telfairi	ENSETEG00000008002	2 retrocopies	retro_etel_1926, retro_etel_1979,
Felis catus	ENSFCAG00000002240	1 retrocopy	retro_fcat_20,
Homo sapiens	ENSG00000101888	1 retrocopy	retro_hsap_80,
Gorilla gorilla	ENSGGOG00000013593	1 retrocopy	retro_ggor_67,
Loxodonta africana	ENSLAFG00000007116	1 retrocopy	retro_lafr_124,
Microcebus murinus	ENSMICG00000014511	3 retrocopies	retro_mmur_149, retro_mmur_1531, retro_mmur_25,
Myotis lucifugus	ENSMLUG00000000631	3 retrocopies	retro_mluc_1513, retro_mluc_160, retro_mluc_473,
Macaca mulatta	ENSMMUG00000013204	1 retrocopy	retro_mmul_140,
Monodelphis domestica	ENSMODG00000021343	1 retrocopy	retro_mdom_1611,
Mustela putorius furo	ENSMPUG00000003973	1 retrocopy	retro_mputfur_74,
Mus musculus	ENSMUSG00000042271	1 retrocopy	retro_mmus_12,
Oryctolagus cuniculus	ENSOCUG00000008261	1 retrocopy	retro_ocun_210,
Procavia capensis	ENSPCAG00000008006	1 retrocopy	retro_pcap_9,
Pongo abelii	ENSPPYG00000020625	1 retrocopy	retro_pabe_101,
Pteropus vampyrus	ENSPVAG00000006149	1 retrocopy	retro_pvam_14,
Rattus norvegicus	ENSRNOG00000019168	2 retrocopies	retro_rnor_2365, retro_rnor_254,
Sorex araneus	ENSSARG00000009307	1 retrocopy	retro_sara_4,
Sus scrofa	ENSSSCG00000012581	1 retrocopy	retro_sscr_8,
Ictidomys tridecemlineatus	ENSSTOG00000005243	3 retrocopies	retro_itri_1138 , retro_itri_141, retro_itri_793,
Tarsius syrichta	ENSTSYG00000001924	1 retrocopy	retro_tsyr_42,
Tursiops truncatus	ENSTTRG00000005115	1 retrocopy	retro_ttru_19,
Vicugna pacos	ENSVPAG00000007314	1 retrocopy	retro_vpac_624,