RetrogeneDB ID: retro_ttru_993

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_914:259902..260884(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EEF1A2
• Ensembl ID: ENSTTRG00000001835
• Aliases: None
• Description: eukaryotic translation elongation factor 1 alpha 2 [Source:HGNC Symbol;Acc:3192]

Sequence

>retro_ttru_993
CAAGAATATGCCCTTCTGGCTAACACTCTGGGCATGAAAGAACTAATTGCCGGAGTTAACAAAATGGATTCCACTGGTCA
CCTTACAGCCAGAAGAGATACAAGAAAATTATTAAGGAATTTAGCACCTACATTAAGAAAATTGGCTACAACTGTGACAC
AGTAGAATTTGTGCCAATTTCTGGCTGGAATGGTGGAACCATGCTGGAGCCAAGTGCTAGCGTGCCCATGGTTCAAGGGA
TGGAAAATCATCTGTAAAGTTGTCAATACCAGTGGAACCACACTGCTTGAAGCTCTGGATTGCATCTTGCCACCAACTTG
TCCAACTGACAAGTCCTTGCATCTGCCCCTCCAGGATGTCTACAAAATTGGTGTTACTGGTACTGTCCCTTTGGGTCGAG
TGGAGACTTGCGTTCTCAAACCTGGCATGGTGGTCACCTTTGCTCCAGTCATTGTTAGAACTGAAGTAAAGTCTGTTGAA
ATGCACCATTAAGTTTTGAGTAAAGCCCTTCCGGGGGACAATGTGGGCTTCAATGTCAAGAGCATGTCTGTCAACTGTGT
TTGTCATGGCAATGTGGCTTGTGACAGCAAAAATGACCCACCGGTGGAAACATCTGGCTTCACAGCTCAAGTGATTATCT
TGAACCATCCAGGACAAATCAGCATTGGATATTCACCTGTGCTGGACTGTCACACAGCTCACATTGCTTACAGGTTTGCT
GAGCTGAAAGAGAAGATTGATCATCAGTCTGGAAAAACAAGCTGGAAGATGTCCCCAAATTCTTGAAATCTGGTGATGTT
GCCATTGTTGATATGCTTCTTGGCAAGCCCATGTGTGTTGTGAACCTCTATGACTATCCTTCTTGTTCATTTGCTGTTCA
TGACATGAGATAAACAGTAACTGTGGATGTCATCAAAGCAGCAGACGAGAAGGCAGCTGGAGTTGACAAGGCACCAGGTC
TGCCCAGAAGGTTCAGAAAGCT

Alignment

ORF - retro_ttru_993 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.97 %
• Parental protein coverage: 70.78 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  REHALLAYTLGVKQLIVGVNKMDSTE-PAYSEKRYDEIVKEVSAYIKKIGYNPATVPFVPISGWHGDNML
          .E.ALLA.TLG.K.LI.GVNKMDST....YS.KRY..I.KE.S.YIKKIGYN..TV.FVPISGW.G..ML
Retrocopy QEYALLANTLGMKELIAGVNKMDSTG<SPYSQKRYKKIIKEFSTYIKKIGYNCDTVEFVPISGWNGGTML

Parental  EPSPNMP-WFKGWKVERKEGNASGVSLLEALDTILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGI
          EPS...P.WFKGWK...K..N.SG..LLEALD.ILPPT.PTDK.L.LPLQDVYKIG..GTVP.GRVET..
Retrocopy EPSASVP>WFKGWKIICKVVNTSGTTLLEALDCILPPTCPTDKSLHLPLQDVYKIGVTGTVPLGRVETCV

Parental  LRPGMVVTFAPVNITTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDIRRGNVCGDSKSDPPQEAAQFT
          L.PGMVVTFAPV...TEVKSVEMHH..LS.ALPGDNVGFNVK..SV.....GNV..DSK.DPP.E...FT
Retrocopy LKPGMVVTFAPVIVRTEVKSVEMHH*VLSKALPGDNVGFNVKSMSVNCVCHGNVACDSKNDPPVETSGFT

Parental  SQVIILNHPGQISAGYSPVIDCHTAHIACKFAEL-EKIDRRSGK-KLEDNPKS-LLSGDAAIVEMVPGKP
          .QVIILNHPGQIS.GYSPV.DCHTAHIA..FAEL.EKID..SGK......P.S.L.SGD.AIV.M..GKP
Retrocopy AQVIILNHPGQISIGYSPVLDCHTAHIAYRFAELKEKIDHQSGKTSWKMSPNS<LKSGDVAIVDMLLGKP

Parental  MCVESFSQYPPLGRFAVRDMRQTVAVGVIKNVEKKSGGAGKV-TKSAQKAQKA
          MCV.....YP....FAV.DMR.TV.V.VIK....K..G..K..T.SAQK.QKA
Retrocopy MCVVNLYDYPSCS-FAVHDMR*TVTVDVIKAADEKAAGVDKA<TRSAQKVQKA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ttru_993 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_993 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus 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 64 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	ENSSTOG00000028862	1 retrocopy	retro_itri_1028,
Tursiops truncatus	ENSTTRG00000000114	19 retrocopies	retro_ttru_1020, retro_ttru_1150, retro_ttru_1196, retro_ttru_1349, retro_ttru_1351, retro_ttru_1368, retro_ttru_1384, retro_ttru_1810, retro_ttru_1861, retro_ttru_1876, retro_ttru_384, retro_ttru_390, retro_ttru_401, retro_ttru_523, retro_ttru_664, retro_ttru_698, retro_ttru_844, retro_ttru_941, retro_ttru_998,
Tursiops truncatus	ENSTTRG00000001835	1 retrocopy	retro_ttru_993 ,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,