RetrogeneDB ID: retro_meug_316

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold100894:399..1529(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EEF1A2
• Ensembl ID: ENSMEUG00000005018
• Aliases: None
• Description: eukaryotic translation elongation factor 1 alpha 2 [Source:HGNC Symbol;Acc:3192]

Sequence

>retro_meug_316
ATGGGCAAAGAAAAGACTCACGTTAAGACTGTTGTCATTGGACATGTAGACTCTGGCAAGTCCACCACTACTGACCACCT
CATCTACAAATGTGGTGGAATTGATTATGAGAACCATTGCAAAGTTTGAGAAGGAGGCTGTTGAGATGGGAAAGGGCTCC
TTTAAATATACCTGGGTCTTGGATAAACTGAAGGCTGAACATGAGCATAGTGTCATTATTGATATCTCCCTATGGAAATT
TGAGACCAGCAAGTACTATGTGACCATTACTGATGATCCAGGAAGCAGAGACTTCATCAAGAACATGATTACAGGCATAT
CTCAGGCAGATTGTGCTGTCCTGCTTGTTGCTGCCAGAGTTGGTGAATTTGAAACTGGTATCTCAAAGAATGAGCAGACC
TGTGAACAGGCCCTTCTGTCTTACACACAATTGATTGTTGGTGTAAAAAAAATGGATTCCACCAAGGCCCCCTACAGCCA
GAAGAGATACAAGGAAATTGTCAAGGAAATCAGTACCTATTAAGAAAATTGACTACAACCCTGATACAGTAGCTTTTTTG
TCAGTTTCAGGTTGGATTGGTGACAAGATGCTGGAGCCAAGTTCTAATATGCCCTGGCTCAAGGGATGGAAAGTCACTCA
TAAGGATGGTAACGCTAATGGAACTACACTGTTTGAAGCTTTGGATTGCATTCTGCCACAAACTTGTGCAAATGACAAGC
CCCTTTGTCTCCTTCAAGATGTCTATAAGCTTGGTGGTATCGGTACTGTACCTGTTGACTGAGTGGAAACTGGTGTTCTA
AAACCAAGCGTGGTGGTCACCTCAGTCAATGTCACAACCGAAGTAAAGTCTGTTGAAATGTGCCATGAAACTTTGAGTGA
GGCTCTGCCAGGGGATAATGTTGGTTTTAGTGTCAAGAACATGTCTCTCAAAGATGTCCACAATGGTAATGTGGCTGGTG
ATAGCAAGAATGACCCACCTATGGAAGCAGCTGGTTTCATTGCACAGGTTATTACCCTGAACCATCCAGGCCAAATCAGT
GCTAGCTATGCACCTGTTCTGGATTGTCACACTGCTTACATAGATTGCAAGTTTATTGAACTGAAGGAGAAGATTGATCA
TCATTCTGGT

Alignment

ORF - retro_meug_316 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.13 %
• Parental protein coverage: 82.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGID-KRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERER
          MGKEKTH...VVIGHVDSGKSTTT.HLIYKCGGID..RTI.KFEKEA.EMGKGSFKY.WVLDKLKAE.E.
Retrocopy MGKEKTHVKTVVIGHVDSGKSTTTDHLIYKCGGID>MRTIAKFEKEAVEMGKGSFKYTWVLDKLKAEHEH

Parental  GITIDISLWKFETTKYYITIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALL
          ...IDISLWKFET.KYY.TI.D.PG.RDFIKNMITG.SQADCAVL.VAA.VGEFE.GISKN.QT.E.ALL
Retrocopy SVIIDISLWKFETSKYYVTITDDPGSRDFIKNMITGISQADCAVLLVAARVGEFETGISKNEQTCEQALL

Parental  AYTLGVKQLIVGINKMDSTEPPYSEKRYDEIVKEVSAY-IKKI-GYNPATVPFVPISGWHGDNMLEPSPN
          .YT....QLIVG....DST..PYS.KRY.EIVKE.S.Y...K...YNP.TV.F...SGW.GD.MLEPS.N
Retrocopy SYT----QLIVGXXXXDSTKAPYSQKRYKEIVKEISTY<LRKL<DYNPDTVAFLSVSGWIGDKMLEPSSN

Parental  MPWFKGWKVERKEGNASGVSLLEALDTILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGILRPGMV
          MPW.KGWKV..K.GNA.G..L.EALD.ILP.T...DKPL.L.LQDVYK.GGIGTVPV..VETG.L.P..V
Retrocopy MPWLKGWKVTHKDGNANGTTLFEALDCILPQTCANDKPLCL-LQDVYKLGGIGTVPVD*VETGVLKPSVV

Parental  VTFAPVNITTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDIRRGNVCGDSKSDPPQEAAQFTSQVIIL
          VT...VN.TTEVKSVEM.HE.LSEALPGDNVGF.VKN.S.KD...GNV.GDSK.DPP.EAA.F..QVI.L
Retrocopy VT--SVNVTTEVKSVEMCHETLSEALPGDNVGFSVKNMSLKDVHNGNVAGDSKNDPPMEAAGFIAQVITL

Parental  NHPGQISAGYSPVIDCHTAHIACKFAELKEKIDRRSG
          NHPGQISA.Y.PV.DCHTA.I.CKF.ELKEKID..SG
Retrocopy NHPGQISASYAPVLDCHTAYIDCKFIELKEKIDHHSG

Legend:

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

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_316 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_316 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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 45 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	ENSTTRG00000001835	1 retrocopy	retro_ttru_993,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,