RetrogeneDB ID: retro_amel_1476

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193466.1:224640..225164(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL18A
• Ensembl ID: ENSAMEG00000010878
• Aliases: None
• Description: 60S ribosomal protein L18a [Source:UniProtKB/TrEMBL;Acc:G1LWI8]

Sequence

>retro_amel_1476
GCCCTGAAGGCCTGGAACACACTGCAAGAGTACAAAGTGGTGGGGTGCTGCCTGCCCACCCCCAGATACGGCACTCCGTC
CCTCTATCACAGGCGAATCTTTGTACCTCGTCATGTTGTCACCAAGTCCTGGTTCTGGTACTTTGTGTCTTTGCTGAAGA
AGATGGAGTCTGCAGGGGAAATTGTCTACTGTGGACAGGTTTTCAAGAAGTCCCACTTGTGGGTGAAGAACTTCACGTGG
CTATGCTCTGACTCCCCTAGGGGCACCCACACATCTACTGGGAGTGCCTGGACCCCACCACTGCAGGCGCTGTCACCTGG
TGCTACTGAAACATGGGCATCCTGCACAGCACCAGGGACCCACTAGATCCAGATCATCCAGGTGGAGGCGATTGCAGCCA
CCAAGTGGCGCAGATCAGCAGTCAAGAGGTTCCACGACTCTGAGATCAAGTTCCTCTGAGCCCCTGAATCATGCATTGTC
ATCACCAGCCATGCTTCACCACCACGAGTCCCAACACCTTCTTT

Alignment

ORF - retro_amel_1476 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.78 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AMKASGTLREYKVVGRCLPTPKCRTPPLYRMRIFAPNHVVAKSRFWYFVSQLKKMKKSSGEIVYCGQVFE
          A.KA..TL.EYKVVG.CLPTP...TP.LY..RIF.P.HVV.KS.FWYFVS.LKKM..S.GEIVYCGQVF.
Retrocopy ALKAWNTLQEYKVVGCCLPTPRYGTPSLYHRRIFVPRHVVTKSWFWYFVSLLKKM-ESAGEIVYCGQVFK

Parental  KSPLRVKNFGIWLRYDSRSGTH-NMYREYRDLTTAGAVTQCYRDMGARHRAR-AHSIQVMKVEEIAASKC
          KS.L.VKNF..WL..DS..GTH...Y.E..D.TTAGAVT.CY..MG..H..R..H.IQ...VE.IAA.K.
Retrocopy KSHLWVKNF-TWLCSDSPRGTH<HIYWECLDPTTAGAVTWCY*NMGILHSTR>TH*IQIIQVEAIAATKW

Parental  RRPAVKQFHDSKIKF-PLPHRVLRRQHKPRFTTKRPNTFF
          RR.AVK.FHDS.IKF.PL........H.P.FTT..PNTFF
Retrocopy RRSAVKRFHDSEIKF<PLSP*IMHCHHQPCFTTTSPNTFF

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_1476 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1476 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 15 parental genes, and 59 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003125	1 retrocopy	retro_acar_86,
Ailuropoda melanoleuca	ENSAMEG00000010878	5 retrocopies	retro_amel_1046, retro_amel_1476 , retro_amel_1601, retro_amel_280, retro_amel_461,
Bos taurus	ENSBTAG00000015831	5 retrocopies	retro_btau_145, retro_btau_1586, retro_btau_842, retro_btau_917, retro_btau_922,
Canis familiaris	ENSCAFG00000015122	1 retrocopy	retro_cfam_231,
Callithrix jacchus	ENSCJAG00000014006	7 retrocopies	retro_cjac_1628, retro_cjac_2814, retro_cjac_3192, retro_cjac_3906, retro_cjac_4134, retro_cjac_441, retro_cjac_642,
Cavia porcellus	ENSCPOG00000015205	1 retrocopy	retro_cpor_1478,
Equus caballus	ENSECAG00000015258	1 retrocopy	retro_ecab_745,
Gorilla gorilla	ENSGGOG00000002870	8 retrocopies	retro_ggor_1215, retro_ggor_1680, retro_ggor_1868, retro_ggor_1933, retro_ggor_195, retro_ggor_227, retro_ggor_2775, retro_ggor_2940,
Macropus eugenii	ENSMEUG00000003228	2 retrocopies	retro_meug_36, retro_meug_49,
Macaca mulatta	ENSMMUG00000028844	6 retrocopies	retro_mmul_1416, retro_mmul_1591, retro_mmul_2233, retro_mmul_2547, retro_mmul_292, retro_mmul_364,
Monodelphis domestica	ENSMODG00000019167	2 retrocopies	retro_mdom_349, retro_mdom_680,
Mustela putorius furo	ENSMPUG00000015786	4 retrocopies	retro_mputfur_1007, retro_mputfur_1189, retro_mputfur_1574, retro_mputfur_457,
Pongo abelii	ENSPPYG00000009725	10 retrocopies	retro_pabe_1200, retro_pabe_1319, retro_pabe_1620, retro_pabe_2239, retro_pabe_2302, retro_pabe_3680, retro_pabe_3717, retro_pabe_3802, retro_pabe_482, retro_pabe_487,
Pan troglodytes	ENSPTRG00000010686	3 retrocopies	retro_ptro_1078, retro_ptro_1803, retro_ptro_27,
Sarcophilus harrisii	ENSSHAG00000000406	3 retrocopies	retro_shar_435, retro_shar_474, retro_shar_706,