RetrogeneDB ID: retro_itri_1028

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393360.1:499061..500317(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EEF1A2
• Ensembl ID: ENSSTOG00000028862
• Aliases: None
• Description: eukaryotic translation elongation factor 1 alpha 2 [Source:HGNC Symbol;Acc:3192]

Sequence

>retro_itri_1028
CCACCGCTAAATCGAAGCCAAAATGGGAAAAGAAAATATATCAACATCATTGTCATTGGACACGTAGATTCAGGCAAGTC
TACCACTACTGGCCATCTGATCTACAAAAGTGATGGGATGGACAAAAGAATCATTGAAAAATTTGAGAAGGAAGCTGCTG
AGATGGGAAAGTGCTCCTTCAAGTATGCCTGGGTCTTGGATAAACTGAAAGCTGAACGTGACTGTGGTATCACCATTGAC
ATCTCCCTGTGGAAATTTGAGACCAGCAAGTATTATGTGACTATCATTAATGCCCCAGGACACAGACTTTATCAAAAACA
TGAATACAGGCACATCTCAGGCTGACTGTGCTGTCCTGATTGTTGCTGCTGGCATTGGTGAATTTGAAGCTGGTATCTCC
AAGAATGGGCAGACCCGTGAACATGTCCTTCTGGCCTACACACTGGGTGTGAAACAACTAATCGTTGGTGTTAACAAAAT
GGATTCCACTGAGCCACTCTACAGTCAGAAGAGATATGAGGAAATTGTCAAGGAAGTCAGCATCTACATTAAGAAAATTG
GCTACAACACTGACACACTAGCATTTGTGCCAATTTCTGGTTGGAATGGTGACAACATGTTGGAACCAAGTGCTAATATG
CCTTGGTTCAAGGGATGGAAAGTCACCTGTAAAGATGGCAGTGCCAATGGAACCACATTGCTTGAAGCTTTAGATTGCAT
CCTGCCACCAACTCATCCAACTGACAAGCCTTTGCGTCTGCCCCTCCAGGATGTCTACAAAATTGGTGGTATTGGTACTG
TCCCTGTGGGCCGAGTGGAGACTGGTATTCTCAAGCCTGGCATGGTGGTCACCTTTGCTCCAGTCAATGTCACAACTGAA
GTAAAGTCTGTTGAAATGCACCATGAAGCTCTGAATGAAGCTCTTCCTGGAGACAATATAGACTTCAATGTTAAGAACGT
GTCTGTCAAAGATGTTTGTCGTGGCAATGTTGCTAGTGACAGCAAAAATGACCCACCAATGGAAGCAGCTGGTTCCACTG
CTCAGGTGATTATCCTGAACCATCCGGGCCAAATCAGCGCTGGCTATGCTCCTATACTGGATTGTCACACAGCTCACATT
GCTTGCAAGTTTGCCGAGCTGAAAGAAAAGATTGATTGCCATTCTAGTAAGAAGCTGGAAGATGGCCCTAAATTCTTGAA
ATCTGGTGATGCTGCCATCGTTGATAATGGTTCCAGGAAAACCCATCTGTGTTGAG

Alignment

ORF - retro_itri_1028 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.99 %
• Parental protein coverage: 97.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PPWQQGKMGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKL
          PP......GK.K..INI.VIGHVDSGKSTTTGHLIYK..G.DKR.IEKFEKEAAEMGK.SFKYAWVLDKL
Retrocopy PPLNRSQNGKRK-YINIIVIGHVDSGKSTTTGHLIYKSDGMDKRIIEKFEKEAAEMGKCSFKYAWVLDKL

Parental  KAERERGITIDISLWKFETTKYYITIID-APGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQ
          KAER..GITIDISLWKFE.T..Y...I...P...DFIKNM.TGTSQADCAVLIVAAG.GEFEAGISKNGQ
Retrocopy KAERDCGITIDISLWKFE-TSKYYVTII>MPQDTDFIKNMNTGTSQADCAVLIVAAGIGEFEAGISKNGQ

Parental  TREHALLAYTLGVKQLIVGVNKMDSTEPAYSEKRYDEIVKEVSAYIKKIGYNPATVPFVPISGWHGDNML
          TREH.LLAYTLGVKQLIVGVNKMDSTEP.YS.KRY.EIVKEVS.YIKKIGYN..T..FVPISGW.GDNML
Retrocopy TREHVLLAYTLGVKQLIVGVNKMDSTEPLYSQKRYEEIVKEVSIYIKKIGYNTDTLAFVPISGWNGDNML

Parental  EPSPNMPWFKGWKVERKEGNASGVSLLEALDTILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGIL
          EPS.NMPWFKGWKV..K.G.A.G..LLEALD.ILPPT.PTDKPLRLPLQDVYKIGGIGTVPVGRVETGIL
Retrocopy EPSANMPWFKGWKVTCKDGSANGTTLLEALDCILPPTHPTDKPLRLPLQDVYKIGGIGTVPVGRVETGIL

Parental  RPGMVVTFAPVNITTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDIRRGNVCGDSKSDPPQEAAQFTS
          .PGMVVTFAPVN.TTEVKSVEMHHEAL.EALPGDN..FNVKNVSVKD..RGNV..DSK.DPP.EAA..T.
Retrocopy KPGMVVTFAPVNVTTEVKSVEMHHEALNEALPGDNIDFNVKNVSVKDVCRGNVASDSKNDPPMEAAGSTA

Parental  QVIILNHPGQISAGYSPVIDCHTAHIACKFAELKEKIDRRSGKKLEDNPKSLKSGDAAIVE-MVPGKPMC
          QVIILNHPGQISAGY.P..DCHTAHIACKFAELKEKID..S.KKLED.PK.LKSGDAAIV..MVPGKP.C
Retrocopy QVIILNHPGQISAGYAPILDCHTAHIACKFAELKEKIDCHSSKKLEDGPKFLKSGDAAIVD>MVPGKPIC

Parental  VE
          VE
Retrocopy VE

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_1028 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1028 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 14 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013249	1 retrocopy	retro_cfam_1007,
Equus caballus	ENSECAG00000022260	1 retrocopy	retro_ecab_802,
Latimeria chalumnae	ENSLACG00000002952	1 retrocopy	retro_lcha_39,
Loxodonta africana	ENSLAFG00000028081	1 retrocopy	retro_lafr_651,
Macropus eugenii	ENSMEUG00000005018	23 retrocopies	retro_meug_1067, retro_meug_110, retro_meug_1160, retro_meug_1240, retro_meug_1334, retro_meug_135, retro_meug_1421, retro_meug_1451, retro_meug_1465, retro_meug_1501, retro_meug_1662, retro_meug_1690, retro_meug_1710, retro_meug_1829, retro_meug_2023, retro_meug_2044, retro_meug_2050, retro_meug_316, retro_meug_601, retro_meug_755, retro_meug_792, retro_meug_850, retro_meug_920,
Myotis lucifugus	ENSMLUG00000016760	1 retrocopy	retro_mluc_1250,
Mustela putorius furo	ENSMPUG00000008289	3 retrocopies	retro_mputfur_1030, retro_mputfur_609, retro_mputfur_761,
Nomascus leucogenys	ENSNLEG00000010060	2 retrocopies	retro_nleu_11, retro_nleu_1489,
Ornithorhynchus anatinus	ENSOANG00000004908	1 retrocopy	retro_oana_73,
Otolemur garnettii	ENSOGAG00000004630	8 retrocopies	retro_ogar_1067, retro_ogar_2034, retro_ogar_2329, retro_ogar_2497, retro_ogar_2583, retro_ogar_3191, retro_ogar_3270, retro_ogar_643,
Ictidomys tridecemlineatus	ENSSTOG00000007687	4 retrocopies	retro_itri_1509, retro_itri_1740, retro_itri_1816, retro_itri_195,
Ictidomys tridecemlineatus	ENSSTOG00000028862	1 retrocopy	retro_itri_1028 ,
Tursiops truncatus	ENSTTRG00000001835	1 retrocopy	retro_ttru_993,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,