RetrogeneDB ID: retro_meug_411

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold11111:11693..12865(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5B
• Ensembl ID: ENSMEUG00000002875
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide [Source:HGNC Symbol;Acc:830]

Sequence

>retro_meug_411
GAGACCTTAGGAAGAATCATGAATGTGATTGGAGAGCCTATCGATGAAAGGGTTCCAATAAAAACCAAAGTTTGCTGCTA
TTCATGCTGAGGCTCCTGAATTCATAAAGATGAGTGTAGAGAAAGAAATCCTGGTCACTGGCATCAAAGTTGTGGATCTT
TTGGCCCCATATGCCAAGGGTGGCAGAATTGGTCTCTTTGGTGGTGCTGGTGTGGGAAAGACAGTATTGATTATGGAACT
AATCAACAATGTTTGGCAAAGTCCATGGTGGTTATTCTGTATTTGCTGGTGTAGGGGAACGGACTCGAGAAGGCAATGAC
TTTTACCACGAGATGATTGAGTCTGGTGTCATCAATCTGAAGGATGCCACTTCCAAGGTAGCATTGGTATATGGCCAAAT
GAATGAACCACCTGGTGCTCAAGCTCGGGTAGCTTTGACTGCCCTCACTGTGGCTGAATAGTTCAGAGATCAAGAGGGTC
CAGATGTATTGCTCTTCATTGGTAATATCTTCTGATTCACTCAGGCTGGCTCAGAGGTGTCTGCTTTACTAAGCAGAATC
CCCTCTGCTGTTGGTTACCAACCCACTTTGGCCACTGATATGGGCACCATGCAGGAAAGAATTACCACAACCAAGAAAGG
TTCTATCACCTCTGTACAAGCCATCTATGTCCCTGCTGATGACTTGACTGACCCTGCTCCTGCCACCACCTTTGCCCACT
TGGGTGCTACCACTGTGCTGTTCTGGACTATTGCTGAGCCCCAGCTCATTTACCCTGCAGTGGATCCTCTGGACTCCACT
TCCTGGATCATGGACCCCAACATTGTTGGCAATGAGCACTATGATGTTGCCTGAGGTGTGCAATAGATTCTGCAGGACTA
TAAATCCCTCCAGGACATCATTGCTATCCTTGGTATGGATGAGCTGTCTGAAGAAGATAAGTTGACAGCGTCTGGGGCCC
GGAAAATCCAGTGTTTCATGTCACAGCCATTCCAAGTTGCTGAGGTATTCACAGGACATATGGGGAAGTTGGTACCCCTG
AAAGAAGCTATTAAGGGATTCCAGCAAATCTTGGCAGGTCAGTAAGACCATCTCCCAGAGCAGGCCTTCTATATGGTCAG
ACCCACTGAAGAAGCTGTGACAAAAGCTGAAAAATTGGCTGAAGAGCACTCG

Alignment

ORF - retro_meug_411 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.82 %
• Parental protein coverage: 73.86 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ETLGRIMNVIGEPIDERGPI-KTKQFAAIHAEAPEFVEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGG
          ETLGRIMNVIGEPIDER.PI.K.K.FAAIHAEAPEF..MSVE.EILVTGIKVVDLLAPYAKGG.IGLFGG
Retrocopy ETLGRIMNVIGEPIDERVPI>KPK-FAAIHAEAPEFIKMSVEKEILVTGIKVVDLLAPYAKGGRIGLFGG

Parental  AGVGKTVLIMELINNV-AKAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDTTSKVALVYGQMNEPP
          AGVGKTVLIMELINNV..K.HGGYSVFAGVGERTREGND.YHEMIESGVINLKD.TSKVALVYGQMNEPP
Retrocopy AGVGKTVLIMELINNV>GKVHGGYSVFAGVGERTREGNDFYHEMIESGVINLKDATSKVALVYGQMNEPP

Parental  GARARVALTGLTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQERI
          GA.ARVALT.LTVAE.FRDQEG.DVLLFI.NIF.FTQAGSEVSALL.RIPSAVGYQPTLATDMGTMQERI
Retrocopy GAQARVALTALTVAE*FRDQEGPDVLLFIGNIF*FTQAGSEVSALLSRIPSAVGYQPTLATDMGTMQERI

Parental  TTTKKGSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELG-IYPAVDPLDSTSRIMDPNIVGN
          TTTKKGSITSVQAIYVPADDLTDPAPATTFAHL.ATTVL...IAE...IYPAVDPLDSTS.IMDPNIVGN
Retrocopy TTTKKGSITSVQAIYVPADDLTDPAPATTFAHLGATTVLFWTIAEPQLIYPAVDPLDSTSWIMDPNIVGN

Parental  EHYDVARGVQKILHDYKSLQDIIAILGMDELSEEDKLTVSRARKIQRFLSQPFQVAEVFTGHLGKLVPLK
          EHYDVA.GVQ.IL.DYKSLQDIIAILGMDELSEEDKLT.S.ARKIQ.F.SQPFQVAEVFTGH.GKLVPLK
Retrocopy EHYDVA*GVQ*ILQDYKSLQDIIAILGMDELSEEDKLTASGARKIQCFMSQPFQVAEVFTGHMGKLVPLK

Parental  ETIKGFQQILAGQYDHLPEQAFYMVGPIEEAVTKAEKLAEEHS
          E.IKGFQQILAGQ.DHLPEQAFYMV.P.EEAVTKAEKLAEEHS
Retrocopy EAIKGFQQILAGQ*DHLPEQAFYMVRPTEEAVTKAEKLAEEHS

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_411 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_411 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 17 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016752	1 retrocopy	retro_acar_181,
Bos taurus	ENSBTAG00000013315	1 retrocopy	retro_btau_1264,
Choloepus hoffmanni	ENSCHOG00000005350	1 retrocopy	retro_chof_1544,
Callithrix jacchus	ENSCJAG00000033571	2 retrocopies	retro_cjac_1488, retro_cjac_928,
Dasypus novemcinctus	ENSDNOG00000011289	1 retrocopy	retro_dnov_361,
Echinops telfairi	ENSETEG00000010208	1 retrocopy	retro_etel_2162,
Homo sapiens	ENSG00000110955	1 retrocopy	retro_hsap_2128,
Gorilla gorilla	ENSGGOG00000011596	1 retrocopy	retro_ggor_1648,
Macropus eugenii	ENSMEUG00000002875	6 retrocopies	retro_meug_1416, retro_meug_1608, retro_meug_411 , retro_meug_430, retro_meug_685, retro_meug_908,
Microcebus murinus	ENSMICG00000001084	1 retrocopy	retro_mmur_495,
Macaca mulatta	ENSMMUG00000001027	1 retrocopy	retro_mmul_103,
Pongo abelii	ENSPPYG00000004668	2 retrocopies	retro_pabe_1921, retro_pabe_2032,
Pan troglodytes	ENSPTRG00000005107	1 retrocopy	retro_ptro_1557,
Sus scrofa	ENSSSCG00000000405	1 retrocopy	retro_sscr_453,
Tarsius syrichta	ENSTSYG00000009962	1 retrocopy	retro_tsyr_644,
Tursiops truncatus	ENSTTRG00000002144	1 retrocopy	retro_ttru_371,
Vicugna pacos	ENSVPAG00000004025	2 retrocopies	retro_vpac_405, retro_vpac_562,