RetrogeneDB ID: retro_amel_39

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194758.1:85052..86003(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000018997
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FOXR1
• Ensembl ID: ENSAMEG00000000053
• Aliases: None
• Description: forkhead box R1 [Source:HGNC Symbol;Acc:29980]

Sequence

>retro_amel_39
ATGGACATAAAACTAAAAAATCCTGAATTCTGGTACAGTCTCCATGGCCGGGTCCCAGGGCTGCTGGACTGGGACATGGG
GAATGAGTTCTTCTTGCCCTGCACCACAGACCAATGCCACTTAGCTGAGCAGAACCTTGCCAAATATAGACTCCGAGTAA
TGGAGCCCCCAAAGGTGCCTCAAGAGAGCAGACCCAGTCCAGACAAAGATGGTCCTGACTGTGAATCTAACCTGTGGATG
TGGGTAAATCCAAATATCATGTGCCCCCTTGGCAGCCAGGAGACCCTAAAGCCCAGTAAGGAAAAGAATCTGACAAGAAT
GCTTCCTTACCCTCAGCCACTTCCAAGGGATGAAGAATCTAACTGCTCAAAGGCCACAGTGATGGAGTCCTTGCCAACTT
CCTCCAACAAGAAATCTTCCCCACAGAAGCAGTGCACTTATTCCCCCAGTGACTGGGAGATCACAGAAGAAAAAACTGAG
GAACAAGATGACAACTGCTCTGTGTCCCTTCAATCCCCTAACAAAGGGGAGTGCTTCCAGAACCAGAAGCTATGGCAAGG
CAACAGCCAGGAGAGGAGGTCCTGGCCCCGGCCCCCCCTCAATTACAGTCACCTAATTGCCCTGGCATTAAGAAACAGCC
CCCCCTGTGGCCTCAATGTGCAAGAGATCTACAATTTCACCCGACAGCATTTCCCCTTTTTTTGGACAGCTCCAAATGGC
TGGAAAAACACCATCCGCCACAACCTCTGCTTCCTGGGCAGCTTTGAGAAGGCACCCGTCAACCTTCAGGATGGGACCAA
TGCAAAACCACGGTCTGGCCTCTGGAGGCTTACTGAGGAGGGACATCGCTGCTTTCAGGAGAAGACTCGTGCCTTAGCCT
CTGCTCGGAGGGAGAGCATCCAACAGTGCATGAGCCAGCCAGATGTGATGACCGCCCTCTTTGGCCTTTGA

Alignment

ORF - retro_amel_39 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VDLKLQHLDLWASLHGQVPGLLDWDMGNESFLAFTRCDPCSFCLLLHIIARYRLRIVEPPKVPVEKNPSP
          .D.KL.....W.SLHG.VPGLLDWDMGNE.FL..T..D.C...L.....A.YRLR..EPPKVP.E..PSP
Retrocopy MDIKLKNPEFWYSLHGRVPGLLDWDMGNEFFLPCTT-DQCH--LAEQNLAKYRLRVMEPPKVPQESRPSP

Parental  DNDGPTVEPNLWMWVNPNIVFPPGKLEVPEPRKGEDQPSTLPSPQPPPKEEDLADCSSEATAGESESLPS
          D.DGP..E.NLWMWVNPNI..P.G..E...P.K.......LP.PQP.P..E....CS....A...ESLP.
Retrocopy DKDGPDCESNLWMWVNPNIMCPLGSQETLKPSKEKNLTRMLPYPQPLPRDEE-SNCSK---ATVMESLPT

Parental  SS-EQSPPRKRMRFASSPSTWELAEEEAADQDDSSSVALPSPHKRAPLQSQRPRQASSQEGRLWSRPPLN
          SS...S.P.K......SPS.WE..EE....QDD..SV.L.SP.K....Q.Q...Q..SQE.R.W.RPPLN
Retrocopy SSNKKSSPQKQCTY--SPSDWEITEEKTEEQDDNCSVSLQSPNKGECFQNQKLWQGNSQERRSWPRPPLN

Parental  YFHLIALALRNSSPCGLNVQQIYNFTRQHFPFFRTAPEGWKNTVRHNLCFRDSFEKVPVSMQAGASVRPR
          Y.HLIALALRNS.PCGLNVQ.IYNFTRQHFPFF.TAP.GWKNT.RHNLCF..SFEK.PV..Q.G....PR
Retrocopy YSHLIALALRNSPPCGLNVQEIYNFTRQHFPFFWTAPNGWKNTIRHNLCFLGSFEKAPVNLQDGTNAKPR

Parental  SCLWKLTKEGHRRFAEEARALASTHLESIQQCMSQPDVMPFLFDL
          S.LW.LT.EGHR.F.E..RALAS...ESIQQCMSQPDVM..LF.L
Retrocopy SGLWRLTEEGHRCFQEKTRALASARRESIQQCMSQPDVMTALFGL

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_39 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_39 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 18 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000053	1 retrocopy	retro_amel_39 ,
Bos taurus	ENSBTAG00000014606	1 retrocopy	retro_btau_189,
Canis familiaris	ENSCAFG00000012417	1 retrocopy	retro_cfam_209,
Callithrix jacchus	ENSCJAG00000013656	1 retrocopy	retro_cjac_4066,
Dasypus novemcinctus	ENSDNOG00000009414	1 retrocopy	retro_dnov_22,
Dipodomys ordii	ENSDORG00000001960	1 retrocopy	retro_dord_651,
Homo sapiens	ENSG00000176302	1 retrocopy	retro_hsap_72,
Microcebus murinus	ENSMICG00000002680	1 retrocopy	retro_mmur_38,
Macaca mulatta	ENSMMUG00000022722	1 retrocopy	retro_mmul_125,
Mustela putorius furo	ENSMPUG00000004890	1 retrocopy	retro_mputfur_161,
Nomascus leucogenys	ENSNLEG00000007376	1 retrocopy	retro_nleu_50,
Otolemur garnettii	ENSOGAG00000007258	1 retrocopy	retro_ogar_296,
Procavia capensis	ENSPCAG00000010132	1 retrocopy	retro_pcap_12,
Pongo abelii	ENSPPYG00000003947	1 retrocopy	retro_pabe_69,
Pan troglodytes	ENSPTRG00000004358	1 retrocopy	retro_ptro_94,
Sorex araneus	ENSSARG00000011319	1 retrocopy	retro_sara_38,
Sus scrofa	ENSSSCG00000015101	1 retrocopy	retro_sscr_36,
Ictidomys tridecemlineatus	ENSSTOG00000014321	1 retrocopy	retro_itri_158,