RetrogeneDB ID: retro_meug_2020

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold8043:14153..15080(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMEUG00000002921
• Aliases: None
• Description: None

Sequence

>retro_meug_2020
ATTTCCTCCTAATACGATCATCAGGCAGAGGAATACCTTCCCAAGTGAATAGAAGTTGCATTTTTGACTATTGAAACAAA
CTTTCAGCTGGACTTACAAGATGGCATAATCCTCTGTGAATTTATAAACAACCTCCAGCCAGCTTCAGTGAAGAAAGTCA
ATGAGTCTTCATTAAACTGGCCTCAGTTGGAGAACATCTGCAATTTTGTCAAAGCTGTTCAGGCTTATGGTATGAAACCT
CATGGCATCTTTGAAGAAAATCATCTTTTTGAGATTGGAAATATAACCCAAGTTCATACTACACTAGTAACTTTTGCAAG
TCTGGCTTTAAAAAGAGGATTCAATGCAACTATTGACATTGGTGTCAAATATGCAGAAAAGCAAGGAAGGTGCTTTGATG
TAGGAACGCTGAAAGTAGGACAAAGTGTAATTGACTTGCAAATGGGAATCAACAAATGTGGCAGCCAGGCAAGAGTGACT
GCCTATGATTCTAGGAGGCATCTTTATGATGCTCAAATGCAAACTGACACGCATTTTGACAAGACAACAATTAGTCTGCA
GAAGGGTACTAACAAAGGAGCCTGTCAGGCTTGAACGTAAGCACCAGATACCAGAAGAGACATCTATGATCCGAAGTTAA
CATTACAGCCAGTGGACAACTCTGCAATTTCACTACAGATGGATAGCAACAAAGTTGCTTCCCAAAAAGGAATGAGTGTT
TATGGGCTTTGACAACAAGCATATGATCCCAAATATTGTGCTGCTCCAACAGAACTTGTAATATATAATGGAAGACAAGA
AATAGGAACAAATGGGTCTGAAATCAGTGATAACAATTATCAGGCAGAATGTCGAGATGAACATCATGCAGACTACCAAT
ATGACTATCCAAGAGATTATGAGTATAGCGACCAGGTCACTGATTAT

Alignment

ORF - retro_meug_2020 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.84 %
• Parental protein coverage: 84.01 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IASKYDHQAEEDLRNWIEEVTGLSIGTNFQLGLKDGIILCELINKLQPGSVKKVNESSLNWPQLENIGNF
          I.S.YDHQAEE.L...IE.V..L.I.TNFQL.L.DGIILCE.IN.LQP.SVKKVNESSLNWPQLENI.NF
Retrocopy ISS*YDHQAEEYLPK*IE-VAFLTIETNFQLDLQDGIILCEFINNLQPASVKKVNESSLNWPQLENICNF

Parental  IKAIQAYGMKPHDIFEANDLFENGNMTQVQTTLVALAGLAKTKGFHTTIDIGVKYAEKQARRFDEGKLKA
          .KA.QAYGMKPH.IFE.N.LFE.GN.TQV.TTLV..A.LA...GF..TIDIGVKYAEKQ.R.FD.G.LK.
Retrocopy VKAVQAYGMKPHGIFEENHLFEIGNITQVHTTLVTFASLALKRGFNATIDIGVKYAEKQGRCFDVGTLKV

Parental  GQSVIGLQMGTNKCASQAGMTAYGTRRHLYDPKMQTDKPFDQTTISLQMGTNKGASQAGMLAPGTRRDIY
          GQSVI.LQMG.NKC.SQA..TAY..RRHLYD..MQTD..FD.TTISLQ.GTNKGA.QA...AP.TRRDIY
Retrocopy GQSVIDLQMGINKCGSQARVTAYDSRRHLYDAQMQTDTHFDKTTISLQKGTNKGACQA*T*APDTRRDIY

Parental  DQKLTLQPVDNSTISLQMGTNKVASQKGMSVYGLGRQVYDPKYCAAPTEPVIHNGSQGTGTNGSEISDND
          D.KLTLQPVDNS.ISLQM..NKVASQKGMSVYGL..Q.YDPKYCAAPTE.VI.NG.Q..GTNGSEISDN.
Retrocopy DPKLTLQPVDNSAISLQMDSNKVASQKGMSVYGL*QQAYDPKYCAAPTELVIYNGRQEIGTNGSEISDNN

Parental  YQAEYPDDYHVEYQDDYPRDYEYSDQGIDY
          YQAE..D..H..YQ.DYPRDYEYSDQ..DY
Retrocopy YQAECRDEHHADYQYDYPRDYEYSDQVTDY

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_2020 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_2020 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 20 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016707	1 retrocopy	retro_amel_1412,
Bos taurus	ENSBTAG00000020345	1 retrocopy	retro_btau_1211,
Callithrix jacchus	ENSCJAG00000018128	3 retrocopies	retro_cjac_1331, retro_cjac_533, retro_cjac_861,
Dasypus novemcinctus	ENSDNOG00000012883	3 retrocopies	retro_dnov_223, retro_dnov_403, retro_dnov_815,
Equus caballus	ENSECAG00000020188	1 retrocopy	retro_ecab_655,
Echinops telfairi	ENSETEG00000010095	1 retrocopy	retro_etel_638,
Homo sapiens	ENSG00000117519	1 retrocopy	retro_hsap_3419,
Gorilla gorilla	ENSGGOG00000013870	1 retrocopy	retro_ggor_2312,
Macropus eugenii	ENSMEUG00000002921	2 retrocopies	retro_meug_2020 , retro_meug_42,
Macropus eugenii	ENSMEUG00000006573	9 retrocopies	retro_meug_1092, retro_meug_1242, retro_meug_128, retro_meug_1442, retro_meug_1998, retro_meug_309, retro_meug_483, retro_meug_690, retro_meug_880,
Macaca mulatta	ENSMMUG00000001690	1 retrocopy	retro_mmul_1747,
Monodelphis domestica	ENSMODG00000004326	1 retrocopy	retro_mdom_442,
Mustela putorius furo	ENSMPUG00000003332	1 retrocopy	retro_mputfur_896,
Mus musculus	ENSMUSG00000053931	2 retrocopies	retro_mmus_1052, retro_mmus_2544,
Nomascus leucogenys	ENSNLEG00000011207	5 retrocopies	retro_nleu_122, retro_nleu_1342, retro_nleu_2698, retro_nleu_480, retro_nleu_668,
Pan troglodytes	ENSPTRG00000000979	15 retrocopies	retro_ptro_1061, retro_ptro_1149, retro_ptro_1247, retro_ptro_1447, retro_ptro_1505, retro_ptro_1554, retro_ptro_1871, retro_ptro_215, retro_ptro_2323, retro_ptro_2377, retro_ptro_2831, retro_ptro_2894, retro_ptro_3007, retro_ptro_483, retro_ptro_653,
Sorex araneus	ENSSARG00000012874	1 retrocopy	retro_sara_582,
Sarcophilus harrisii	ENSSHAG00000002670	1 retrocopy	retro_shar_567,
Tarsius syrichta	ENSTSYG00000010749	2 retrocopies	retro_tsyr_1458, retro_tsyr_1907,
Vicugna pacos	ENSVPAG00000004889	2 retrocopies	retro_vpac_190, retro_vpac_449,