RetrogeneDB ID: retro_itri_747

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393317.1:4395458..4396784(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OXCT1
• Ensembl ID: ENSSTOG00000008271
• Aliases: None
• Description: 3-oxoacid CoA transferase 1 [Source:HGNC Symbol;Acc:8527]

Sequence

>retro_itri_747
GGAATTCCAGAGAATCTTATAGGAGCTTTATTGAAGACTAGAGCTAAAGGATTAACTGCAGTCAGCAACAGTGCAGGGGT
TGAGGACTTTGGCGTGGGTCTGCTGCTTCGATCCAAGCAAATCAAACGCATGGTCTCTTCCTACGTGGGAGAAAATGCCG
ACTTTGAACGGCAGTTTTTATCTGGTGACTTAGAAGTGGAGCTGACACCTCAGGGCACCCTTGCGGAGAAAATCCGTGCC
GGTGGTGCTGGAGTTCCTGCGTTTTACACCCGCACAGGGTACGGGACCCTGGTTCAAGAAGGGGGAGCACCCATCAAATA
CAACAAAGATGGCAGCATCGCTATTGCCAGTAAGCCCAGGGAGGTGAGAAAGTTTAATGGTCAGCACTTTGTTTTGGAAG
AAGCAATTACAGGGGATTTTGCTTTGGTGAAAGCCTGGAAAGCCGATCGATCAGGAAACGTGATTTTCAGGAAAAGTGCG
AGGAACTTCAACCAGCCCATGTGCAAAGCTGCAGAAACCACAGTGGTAGAGGTTGAAGAAATTGTGGATGTTGGGTCATT
TGCTCCAGAAGACGTCCACATTCCTAAGATTTATGTCCATCGCATTATAAAGGGAGAAAAATACGAGAAAAGAATTGAGC
GTCGAACAATCCGGAAGGAAGGAGATGGAAAAATCAAATCTGGTAAACCTGCAAGCAATGTAAGGGAACGGATCATCAAA
CGAGCAGCTCTTGAATTTGAGGATGGCATGTACGCTAATTTGGGTATAGGAATCCCTCTTCTGGCCAGCAACTTCATCAG
CCCAAATATAACTGTTCATCTTCACTGTGAAAATGGAGTCCTGGGTTTGGGTCCGTATCCATTTGAACATGAAGTTGATG
CAGATCTAATCAATGCAGGCAAGGAAACAGTTACTGTTCTTCCGGGAGCCTCTTTTTTCTCCAGCGATGAGTCATTCGCA
ATGATTAGAGGGGGACATGTCAATCTAACAATGTTAGGAGCAATGCAGGTTTCCAGATATGGTGACCTGGCTAACTGGAT
GATACCTAGAAAGGTGGTGAAAGGAATGGGAGGTGCTATGGATTTAGTGTCCAGTGCCAAAACCAAAGTGGTGGTCACAA
TGAAGCATTCTGCAAAGGGAAGTGCCCACAAAATCATGGATAAATGTACGTTCCCCCTGACTGGCAAACAGTGTGTCAAC
CGCATCATCACAGAGAAGGCTGTGTTTGATGTGGACAGTAAGAAAGGGCTGACTCTGATTGAGCTCTGGGAAGGCTTGAC
AGTGGACGACATACAAAAGTGCACTGGGTGTGATTTTGCTGTTTCA

Alignment

ORF - retro_itri_747 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.95 %
• Parental protein coverage: 86.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GIPENLIGALLKTGVKGLIAVSNNAGVDNFGLGLLLRSKQIKRMVSSYVGENAEFERQFLSGELEVELTP
          GIPENLIGALLKT..KGL.AVSN.AGV..FG.GLLLRSKQIKRMVSSYVGENA.FERQFLSG.LEVELTP
Retrocopy GIPENLIGALLKTRAKGLTAVSNSAGVEDFGVGLLLRSKQIKRMVSSYVGENADFERQFLSGDLEVELTP

Parental  QGTLAERIRAGGAGVPAFYTSTGYGTLVQEGGAPIKYNKDGSIAIASKPREVREFNGQHFILEEAITGDF
          QGTLAE.IRAGGAGVPAFYT.TGYGTLVQEGGAPIKYNKDGSIAIASKPREVR.FNGQHF.LEEAITGDF
Retrocopy QGTLAEKIRAGGAGVPAFYTRTGYGTLVQEGGAPIKYNKDGSIAIASKPREVRKFNGQHFVLEEAITGDF

Parental  ALVKAWKADRAGNVIFRKSARNFNLPMCKAADTTVVEVEEIVDVGSFAPEDIHIPKIYVHRLIKGEKYEK
          ALVKAWKADR.GNVIFRKSARNFN.PMCKAA.TTVVEVEEIVDVGSFAPED.HIPKIYVHR.IKGEKYEK
Retrocopy ALVKAWKADRSGNVIFRKSARNFNQPMCKAAETTVVEVEEIVDVGSFAPEDVHIPKIYVHRIIKGEKYEK

Parental  RIERLSTRKEEDGKGRSGKPESNVRERIIKRAALEFEDGMYANLGIGIPLLASNFISPNMTVHLQSENGV
          RIER...RKE.DGK..SGKP.SNVRERIIKRAALEFEDGMYANLGIGIPLLASNFISPN.TVHL..ENGV
Retrocopy RIERRTIRKEGDGKIKSGKPASNVRERIIKRAALEFEDGMYANLGIGIPLLASNFISPNITVHLHCENGV

Parental  LGLGPYPFQHEVDADLINAGKETVTVLPGASFFSSDESFAMIRGGHVDLTMLGAMQVSKYGDLANWMIPG
          LGLGPYPF.HEVDADLINAGKETVTVLPGASFFSSDESFAMIRGGHV.LTMLGAMQVS.YGDLANWMIP.
Retrocopy LGLGPYPFEHEVDADLINAGKETVTVLPGASFFSSDESFAMIRGGHVNLTMLGAMQVSRYGDLANWMIPR

Parental  KMVKGMGGAMDLVSSAKTKVVVTMEHSAKGNVHKIMEKCTLPLTGKECVNRIITEKAVFDVDSKKGLTLI
          K.VKGMGGAMDLVSSAKTKVVVTM.HSAKG..HKIM.KCT.PLTGK.CVNRIITEKAVFDVDSKKGLTLI
Retrocopy KVVKGMGGAMDLVSSAKTKVVVTMKHSAKGSAHKIMDKCTFPLTGKQCVNRIITEKAVFDVDSKKGLTLI

Parental  ELWEGLTVDDIQKSTGCDFAVS
          ELWEGLTVDDIQK.TGCDFAVS
Retrocopy ELWEGLTVDDIQKCTGCDFAVS

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_747 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_747 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.

---

Parental genes homology:

Parental genes homology involve 16 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000033186	2 retrocopies	retro_btau_1243, retro_btau_1302,
Dipodomys ordii	ENSDORG00000016318	1 retrocopy	retro_dord_282,
Equus caballus	ENSECAG00000018312	1 retrocopy	retro_ecab_511,
Homo sapiens	ENSG00000083720	1 retrocopy	retro_hsap_14,
Gorilla gorilla	ENSGGOG00000025087	1 retrocopy	retro_ggor_378,
Myotis lucifugus	ENSMLUG00000009431	1 retrocopy	retro_mluc_194,
Nomascus leucogenys	ENSNLEG00000016656	1 retrocopy	retro_nleu_2438,
Oryctolagus cuniculus	ENSOCUG00000009231	1 retrocopy	retro_ocun_672,
Otolemur garnettii	ENSOGAG00000009909	2 retrocopies	retro_ogar_2773, retro_ogar_2781,
Pongo abelii	ENSPPYG00000015428	2 retrocopies	retro_pabe_336, retro_pabe_478,
Pan troglodytes	ENSPTRG00000016829	1 retrocopy	retro_ptro_140,
Rattus norvegicus	ENSRNOG00000043094	2 retrocopies	retro_rnor_2177, retro_rnor_2256,
Ictidomys tridecemlineatus	ENSSTOG00000008271	1 retrocopy	retro_itri_747 ,
Tarsius syrichta	ENSTSYG00000013641	1 retrocopy	retro_tsyr_1455,
Tursiops truncatus	ENSTTRG00000004331	1 retrocopy	retro_ttru_875,
Vicugna pacos	ENSVPAG00000002550	1 retrocopy	retro_vpac_556,