RetrogeneDB ID: retro_amel_21

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193188.1:742294..743287(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000020261
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SEPHS1
• Ensembl ID: ENSAMEG00000013555
• Aliases: None
• Description: selenophosphate synthetase 1 [Source:HGNC Symbol;Acc:19685]

Sequence

>retro_amel_21
ATGGACTCCTGCGTCATACCCCTGAGACACGGGGGCCTGTCACTGGTGCAGACCACGGATTTCTTTTACCCCTTGGTGGA
AGATCCCTACATGATGGGGCGCATAGCGTGTGCCAACGTGCTGAGTGACCTCTACGCCATGGGCATTACTGAATGTGACA
ACATGTTGATGTTACTCAGCGTCAGCCAGAGTATGACCGAGGAGGAACGAGAAAAGATAACACCACTCATGATCAAAGGC
TTTCGCGATGCTGCTGAGGAAGGAGGGACTGCAGTGACTGGTGGACAGACGGTGGTAAACCCTTGGATTATCGTCGGTGG
GGTTGCCACTGTGGTATGTCAGCCAAATGAATTCATCATGCCTGACAGTGCAGTTGTTGGCGATGTGCTCGTGTTAACCA
AACCCTTAGGAACCCAAGTTGCTGTCAATGCCCACCAGTGGCTGGATAATCCTGAGAGATGGAATAAAATAAATATGGTA
GTCTCCAGAGAAGAGGTAGAGCTGGCTTATCAGGAAGCCATGTTCAATATGGCTACCCTAAACAGGACTGCTGCTGGATT
AATGCACACGTTTAACGCACACGCAGCCACAGATATCACAGGCTTTGGCATTCTAGGACACTCTCAGAACCTTGCGAAAC
AACAAAGAAATGAGGTGTCCTTTGTGATTCATAATCTGCCAATTATTGCCAAGATGGCTGCCATCAGCAAGGCCAGTGGG
CGCTTTGGGCTCCTTCAAGGAACCTCAGCGGAAACTTCTGGGGGATTACTGATTTGTCTGCCAAGAGAACAAGCAGCTCG
CTTTTGTTCTGAAATAAAGTCTTCCAAGTATGGAGAGGGTCACCAAGCATGGATTGTCGGTATTGTGGAAAAGGGAAACC
GGACAGCCCGGATCATTGACAAGCCTCGAGTTATTGAGGTCCTACCTCGTGGGGCCACTGCTACTGCTCTCGCTCCTGAC
AGTTCCAACGCCTCCTCTGAGCCTAGTTCGTGA

Alignment

ORF - retro_amel_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.48 %
• Parental protein coverage: 80.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDTCVIPLRHGGLSLVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLGISNKMTDRER
          MD.CVIPLRHGGLSLVQTTD..YP.V.DPYMMGRIACANVLSDLYAMG.TECDNMLMLL..S..MT..ER
Retrocopy MDSCVIPLRHGGLSLVQTTDFFYPLVEDPYMMGRIACANVLSDLYAMGITECDNMLMLLSVSQSMTEEER

Parental  DKVMPLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMPDNAVPGDVLVLTKPLGTQV
          .K..PL.I.GF.DAAEE.GT.VTGGQTV.NPWI..GGVAT.VCQPNEFIMPD.AV.GDVLVLTKPLGTQV
Retrocopy EKITPLMIKGFRDAAEEGGTAVTGGQTVVNPWIIVGGVATVVCQPNEFIMPDSAVVGDVLVLTKPLGTQV

Parental  AVAVHQWLDIPEKWNKIKLVVTQEDVELAYQEAMMNMARLNRTAAGLMHTFNAHAATDITGFGILGHAQN
          AV..HQWLD.PE.WNKI..VV..E.VELAYQEAM.NMA.LNRTAAGLMHTFNAHAATDITGFGILGH.QN
Retrocopy AVNAHQWLDNPERWNKINMVVSREEVELAYQEAMFNMATLNRTAAGLMHTFNAHAATDITGFGILGHSQN

Parental  LAKQQRNEVSFVIHNLPVLAKMAAVSKACGNMFGLMHGTCPETSGGLLICLPREQAARFCAEIKSPKYGE
          LAKQQRNEVSFVIHNLP..AKMAA.SKA.G..FGL..GT..ETSGGLLICLPREQAARFC.EIKS.KYGE
Retrocopy LAKQQRNEVSFVIHNLPIIAKMAAISKASGR-FGLLQGTSAETSGGLLICLPREQAARFCSEIKSSKYGE

Parental  GHQAWIIGIVEKGNRTARIIDKPRIIEVAPQVAT
          GHQAWI.GIVEKGNRTARIIDKPR.IEV.P..AT
Retrocopy GHQAWIVGIVEKGNRTARIIDKPRVIEVLPRGAT

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_21 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_21 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 9 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013555	1 retrocopy	retro_amel_21 ,
Canis familiaris	ENSCAFG00000004743	2 retrocopies	retro_cfam_1787, retro_cfam_250,
Callithrix jacchus	ENSCJAG00000009494	2 retrocopies	retro_cjac_166, retro_cjac_2219,
Loxodonta africana	ENSLAFG00000004670	1 retrocopy	retro_lafr_125,
Macaca mulatta	ENSMMUG00000021233	4 retrocopies	retro_mmul_1607, retro_mmul_2495, retro_mmul_2647, retro_mmul_922,
Nomascus leucogenys	ENSNLEG00000012205	7 retrocopies	retro_nleu_1868, retro_nleu_2211, retro_nleu_234, retro_nleu_2668, retro_nleu_2873, retro_nleu_3004, retro_nleu_327,
Procavia capensis	ENSPCAG00000015617	1 retrocopy	retro_pcap_341,
Rattus norvegicus	ENSRNOG00000018125	1 retrocopy	retro_rnor_59,
Tursiops truncatus	ENSTTRG00000011114	1 retrocopy	retro_ttru_649,