RetrogeneDB ID: retro_amel_1021

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192836.1:759124..760077(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARIH2
• Ensembl ID: ENSAMEG00000013035
• Aliases: None
• Description: ariadne homolog 2 (Drosophila) [Source:HGNC Symbol;Acc:690]

Sequence

>retro_amel_1021
GATGGCATGGGTGTGGGAGTCTTTTGCATAGCTCAGGACCATCCACTCCAAACACCAGAGAACTTCGTTTCTCCATTGCT
GCCTGATGAAGAATTGAGAGACAAATACAGGGTCTACCTCTTCAGGGACTATGTGGAGAGTCATTACCAGCTCCAGCTGT
GCCCTGGTGCAGATTGCCCCCTCGTTATTTGGGTATGGGAGGCCAGAGCTTGCTAAGTACAGTCCAATCAATGCAATGAG
GTCTTCTGTTTCAAGTGTTGTCAGATGTATCATGCCCCCACAGACTATGCCACAATCTGGAAATGGCTCATGAAATGTGC
TCATAACTCTGAAAGAGCCAACTACATAGATGCTCACACCAAAGACTGTTGCAAATGCAACATCCGCATCGAGAAGAACA
AAGGCTGCAGTCACATGCGATGCTCCAACCGTAACCATGACGTCTACTGGGTACGTCTAGGAGATTAGAAAACCCATGGC
AGCAACTACTATGAGTGCAGTTGGTACAAGTAGAACTCTGACATTGTCGACCAGAGCCAGCAAGCCCAGGACAGGAAGGC
CCTCAAGAAGTACTTGTTCTACTTTGAGAGGTGGGAAAACCATAAGAGCTTGCAGCTCGAGGTGCAGATATACCAGCAGA
TTCATGAGGACACTCAGGAGAGGGGCATGAATAATCTGGGGATCTGGAATGACTGGCAGTACCTACAGAATGCTGCCACG
CTCTTGCCCAAGTGCTGATACACCCTGCAGTACATGTGCCCATATAGTTACTACATGAAGTCTGGATCCAGGAAGAAGCT
GTTGGAATACCAGCAGGCTCAGCTGGAGGCTGAGATTGAAACCTGTCAAGGAAAGTGGAGTGTGCAGATAGCTATGACAA
TGGGGACTTAGAGAACCAGATGCACATAGCAGAGCAGTGGAGGAAAAGGCTGCTGAAGGATTTCCACGACACC

Alignment

ORF - retro_amel_1021 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.12 %
• Parental protein coverage: 75.77 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DGVGVGVSCMAQDCPLRTPEDFVFPLLPNEELRDKYRRYLFRDYVESHYQLQLCPGADCPMVIRVQEPRA
          DG.GVGV.C.AQD.PL.TPE.FV.PLLP.EELRDKYR.YLFRDYVESHYQLQLCPGADCP.VI.V.E.RA
Retrocopy DGMGVGVFCIAQDHPLQTPENFVSPLLPDEELRDKYRVYLFRDYVESHYQLQLCPGADCPLVIWVWEARA

Parental  RRVQCNRCNEVFCFKCRQMYHAPTDCATIRKWLTKCADDSETANYISAHTKDCPKCNICIEKNGGCNHMQ
          ..VQ.N.CNEVFCFKC.QMYHAPTD.ATI.KWL.KCA..SE.ANYI.AHTKDC.KCNI.IEKN.GC.HM.
Retrocopy C*VQSNQCNEVFCFKCCQMYHAPTDYATIWKWLMKCAHNSERANYIDAHTKDCCKCNIRIEKNKGCSHMR

Parental  CSKCKHDFCWMCLGDWKTHGSEYYECSRYKENPDIVNQSQQAQAREALKKYLFYFERWENHNKSLQLEAQ
          CS...HD..W..LGD.KTHGS.YYECS.YK.N.DIV.QSQQAQ.R.ALKKYLFYFERWENH.KSLQLE.Q
Retrocopy CSNRNHDVYWVRLGD*KTHGSNYYECSWYK*NSDIVDQSQQAQDRKALKKYLFYFERWENH-KSLQLEVQ

Parental  TYQRIHEKIQERVMNNLGTWIDWQYLQNAAKLLAKCRYTLQYTYPYAYYMESGPRKKLFEYQQAQLEAEI
          .YQ.IHE..QER.MNNLG.W.DWQYLQNAA.LL.KC.YTLQY..PY.YYM.SG.RKKL.EYQQAQLEAEI
Retrocopy IYQQIHEDTQERGMNNLGIWNDWQYLQNAATLLPKC*YTLQYMCPYSYYMKSGSRKKLLEYQQAQLEAEI

Parental  E-NLSWKVERADSYDRGDLENQMHIAEQRRRTLLKDFHDT
          E.NLS.KVE.ADSYD.GDLENQMHIAEQ.R..LLKDFHDT
Retrocopy E<NLSRKVECADSYDNGDLENQMHIAEQWRKRLLKDFHDT

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_1021 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1021 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 12 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013035	1 retrocopy	retro_amel_1021 ,
Callithrix jacchus	ENSCJAG00000003305	1 retrocopy	retro_cjac_1106,
Homo sapiens	ENSG00000177479	1 retrocopy	retro_hsap_1876,
Gorilla gorilla	ENSGGOG00000017134	1 retrocopy	retro_ggor_1373,
Myotis lucifugus	ENSMLUG00000013946	1 retrocopy	retro_mluc_1869,
Mustela putorius furo	ENSMPUG00000014344	1 retrocopy	retro_mputfur_610,
Mus musculus	ENSMUSG00000064145	1 retrocopy	retro_mmus_795,
Nomascus leucogenys	ENSNLEG00000006710	1 retrocopy	retro_nleu_1228,
Oryctolagus cuniculus	ENSOCUG00000017699	1 retrocopy	retro_ocun_1838,
Pongo abelii	ENSPPYG00000013890	1 retrocopy	retro_pabe_1557,
Pan troglodytes	ENSPTRG00000014902	1 retrocopy	retro_ptro_1259,
Ictidomys tridecemlineatus	ENSSTOG00000001766	1 retrocopy	retro_itri_1047,