RetrogeneDB ID: retro_amel_772

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192622.1:1390079..1391385(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EEF1G
• Ensembl ID: ENSAMEG00000006745
• Aliases: None
• Description: eukaryotic translation elongation factor 1 gamma [Source:HGNC Symbol;Acc:3213]

Sequence

>retro_amel_772
ATGGCAGCTGGCACCCTCTACACATACCCTGAAAACTGGAGGCCTTCGAAGCCTTTCATCGCTGCTCAGTACAGCAAGGC
TCAGGTCCCTGTGCTCTCCACACCACCCTACCTCCACTTTGGCCAAACCAACAACACCCCCAAATTTCTCCATAAATTTT
CTGTCAGCAAGTTTCTGGCATTTGACAGTGAAGATTGTTTCTGTGTGTTTGAGAGTAATGCCATTGCCTGCTGTGTCAGC
AATGAGAAACTGTGGGGTAGTACTCCAGAGGCAGCAGCCCCAGTGGTACAGTGGGTGAGCTTTACTGATAGTGACATAGT
GTCCCCAGCCAATACCTGGGTGTTCCCCACTTTGGACATTGTGTACTACAACAAACACTCCAAGGAGAATGCAAAGGAAA
AGGTAAGGCAAATTCTGGGACTAGAGGATGCTCACTTAAAGACAAAGACTTTCCTGGTGGGTGAATGTTTGACACTGGCT
GACATCACCATTGCCTGCATCGTGTTGTGGCTCTATAAACAGGTCCCGGAGCCTTTTTTCCACTAGACCTTCCTTGACAC
CAACCACTGGTTCCTCACCTGGATTTACCAGCCCCAGTTCTGGGCTATTTTGGGGGAGGTGAAAACTCCATGAGAAGATG
GCCCAGGTTGATGCTAAAAAGTTGCAGAGAGCCATCCTGAAAAAGCTATGCAGAAAGAGAAAGGTTCTCGAGAAGAGAAG
CAGAAGCCCCAGGCTGAGTGGAAAGAGGAGAAAAAGTCTGCTGCCCCTGCTCCTGAGGAGGAGACGGGTGAATGTGAGCA
GGTGCTGGCTGCTGAGCCAAAGGCCAAGGATCCCTTTGCTCACCTGCCCAAGAGTACCTTTGTGTTGGATGAATTTAAGT
GCAAATACTCCAAGGAGGACACCCTGTCTGTGGTGCTACTGTATGTTTAGGATCACTTTGATAAGGATGGCTGATCTCTG
TGCTATTCTGAGTGCTGCCTCCCTGAGAGGTCAGCCAGACTTTCATGAGCTGCAACCACTTCACTGGAATGTTCCAGAGG
TTGGACAAACTGAGGAAAAATGCCTTTGCCAGTGTCACTCTCTTTGGAGCCAACAATAGCAGCTCCATTTCTGAAGTCTG
AGTTTTCTAAGGCCAGGATCTTGCCTTTATGCTGAGTCTAGACTGGCAGGTGTACTAAGAGTCAAATACATGGCAGAAAC
TGGATCGTGGCAGTGAGGAGACCCAGACACTGGTTCTAGAGTGCTTTTCCTGGGAGGGGGCCTTCAGCATGTGGGCAAAG
TATTCAATCGGGGAAAGATCTTCAAG

Alignment

ORF - retro_amel_772 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.55 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAAGTLYTYPENWRAFKALIAAQYSGAQVRVLSAPPHFHFGQTNRTPEFLRKFPAGKVPAFEGDDGFCVF
          MAAGTLYTYPENWR..K..IAAQYS.AQV.VLS.PP..HFGQTN.TP.FL.KF...K..AF...D.FCVF
Retrocopy MAAGTLYTYPENWRPSKPFIAAQYSKAQVPVLSTPPYLHFGQTNNTPKFLHKFSVSKFLAFDSEDCFCVF

Parental  ESNAIAYYVSNEELRGSTPEAAAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNKQATENAKEEVRRILG
          ESNAIA..VSNE.L.GSTPEAAA.VVQWVSF.DSDIV.PA.TWVFPTL.I...NK...ENAKE.VR.ILG
Retrocopy ESNAIACCVSNEKLWGSTPEAAAPVVQWVSFTDSDIVSPANTWVFPTLDIVYYNKHSKENAKEKVRQILG

Parental  LLDAHLKTRTFLVGERVTLADITVVCTLLWLYKQVLEPSFRQAFPNTNRWFLTCINQPQFRAVLGEV-KL
          L.DAHLKT.TFLVGE..TLADIT..C..LWLYKQV.EP.F...F..TN.WFLT.I.QPQF.A.LGEV.KL
Retrocopy LEDAHLKTKTFLVGECLTLADITIACIVLWLYKQVPEPFFH*TFLDTNHWFLTWIYQPQFWAILGEV>KL

Parental  CEKMAQFDAKKF-AESQPKKDTPRKEKGSREEKQKPQAERKEEKKAAAPAAPAPEEEMDECEQALAAEPK
          .EKMAQ.DAKK..AES.P.K....KEKGSREEKQKPQAE.KEEKK.AAPA...PEEE..ECEQ.LAAEPK
Retrocopy HEKMAQVDAKKL<AESHPEK-AMQKEKGSREEKQKPQAEWKEEKKSAAPA---PEEETGECEQVLAAEPK

Parental  AKDPFAHLPKSTFVLDEFKRKYSNEDTLSVALPYFWEHFDKDGWSLWYAEYRFPE-ELTQTFMSCNLITG
          AKDPFAHLPKSTFVLDEFK.KYS.EDTLSV.L.Y...HFDKDG.SL.Y.E...PE.E..QTFMSCN..TG
Retrocopy AKDPFAHLPKSTFVLDEFKCKYSKEDTLSVVLLYV*DHFDKDG*SLCYSECCLPE<EVSQTFMSCNHFTG

Parental  MFQRLDKLRKNAFASVILFGTNNSSSISGVWVFRGQELAFPLSPDWQVDYESYTWRKLDPGSEETQTLVR
          MFQRLDKLRKNAFASV.LFG.NNSSSIS.V.VF.GQ.LAF.LS.DWQV..ES.TW.KLD.GSEETQTLV.
Retrocopy MFQRLDKLRKNAFASVTLFGANNSSSISEV*VF*GQDLAFMLSLDWQVY*ESNTWQKLDRGSEETQTLVL

Parental  EYFSWEGAF-QHVGKTFNQGKIFK
          E.FSWEGAF.QHVGK.FN.GKIFK
Retrocopy ECFSWEGAF<QHVGKVFNRGKIFK

Legend:

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

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_772 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_772 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca 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 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006745	1 retrocopy	retro_amel_772 ,
Canis familiaris	ENSCAFG00000015834	6 retrocopies	retro_cfam_1241, retro_cfam_1398, retro_cfam_1862, retro_cfam_478, retro_cfam_638, retro_cfam_653,
Callithrix jacchus	ENSCJAG00000018949	6 retrocopies	retro_cjac_1464, retro_cjac_1770, retro_cjac_1942, retro_cjac_3147, retro_cjac_841, retro_cjac_874,
Equus caballus	ENSECAG00000014334	1 retrocopy	retro_ecab_419,
Latimeria chalumnae	ENSLACG00000014700	1 retrocopy	retro_lcha_82,
Loxodonta africana	ENSLAFG00000003339	1 retrocopy	retro_lafr_381,
Monodelphis domestica	ENSMODG00000007691	1 retrocopy	retro_mdom_68,
Mustela putorius furo	ENSMPUG00000013942	2 retrocopies	retro_mputfur_427, retro_mputfur_944,
Nomascus leucogenys	ENSNLEG00000003528	2 retrocopies	retro_nleu_1510, retro_nleu_681,
Oryctolagus cuniculus	ENSOCUG00000020959	3 retrocopies	retro_ocun_1693, retro_ocun_369, retro_ocun_693,
Pongo abelii	ENSPPYG00000029434	5 retrocopies	retro_pabe_2237, retro_pabe_2378, retro_pabe_2409, retro_pabe_2473, retro_pabe_3690,
Pan troglodytes	ENSPTRG00000003768	3 retrocopies	retro_ptro_1879, retro_ptro_2017, retro_ptro_3159,
Rattus norvegicus	ENSRNOG00000020075	8 retrocopies	retro_rnor_1312, retro_rnor_2126, retro_rnor_2235, retro_rnor_2269, retro_rnor_2468, retro_rnor_2617, retro_rnor_2928, retro_rnor_979,