RetrogeneDB ID: retro_amel_1720

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194087.1:339120..339511(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL13A
• Ensembl ID: ENSAMEG00000014027
• Aliases: None
• Description: None

Sequence

>retro_amel_1720
AACTTCAAAGCACCCAGCCACATCTTTTGGCAGACAGTGCGAAGCATGCTGCCCCACAAGACCAAGAAAAGCCAGGCTGC
CCTGAACCACCTCAAGGTGTTTGCTGGGATACTGCCACTCTATGACAATAAAAAGTGGATAGTGGTCCCTGCTGTCCTAA
GGCTGTGTGTCTGAAACCTACAGAAATTTTGCTTACCTGTGCCACCTGGCTCATGAGGTTGCCTGGAAGCACCAGGCAGT
AATAGCCACTCTGGAGGAGAAGAGGAAAGAGAAGGAAAAGAGCCATTACTAGAAGAAAAAGCAGCTCATGAGGTTATGGA
AACAGTCCAAAAAGAATGTGAAGAAAATTGAGAAGTACACAGAAGTCCTCAAGACCCATAGACTCCTGGTC

Alignment

ORF - retro_amel_1720 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.88 %
• Parental protein coverage: 65.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HFRAPSRIFWRTVRGMLPHKTKRGQAALDRLKVFDGIPPPYDKKKRMVVPAAL-KVVRLKPT-RKFAYLG
          .F.APS.IFW.TVR.MLPHKTK..QAAL..LKVF.GI.P.YD.KK..VVPA.L.K.V.LKPT.R.FAYL.
Retrocopy NFKAPSHIFWQTVRSMLPHKTKKSQAALNHLKVFAGILPLYDNKKWIVVPAVL<KAVCLKPT<RNFAYLC

Parental  RLAHEVGWKYQAVTATLEEKRKEKAKIHYRKKKQLMRLRKQAEKNVEKKIDKYTEVLKTHGLLV
          .LAHEV.WK.QAV.ATLEEKRKEK.K.HY.KKKQLMRL.KQ..KNV.KKI.KYTEVLKTH.LLV
Retrocopy HLAHEVAWKHQAVIATLEEKRKEKEKSHY*KKKQLMRLWKQSKKNV-KKIEKYTEVLKTHRLLV

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_1720 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1720 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 11 parental genes, and 58 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014027	2 retrocopies	retro_amel_1332, retro_amel_1720 ,
Bos taurus	ENSBTAG00000005296	3 retrocopies	retro_btau_1251, retro_btau_719, retro_btau_789,
Canis familiaris	ENSCAFG00000029892	3 retrocopies	retro_cfam_1772, retro_cfam_924, retro_cfam_976,
Callithrix jacchus	ENSCJAG00000000072	16 retrocopies	retro_cjac_1130, retro_cjac_1706, retro_cjac_182, retro_cjac_197, retro_cjac_1997, retro_cjac_2170, retro_cjac_2322, retro_cjac_2467, retro_cjac_2468, retro_cjac_2665, retro_cjac_2699, retro_cjac_2755, retro_cjac_3009, retro_cjac_664, retro_cjac_941, retro_cjac_972,
Echinops telfairi	ENSETEG00000017076	2 retrocopies	retro_etel_46, retro_etel_853,
Loxodonta africana	ENSLAFG00000016213	3 retrocopies	retro_lafr_1160, retro_lafr_576, retro_lafr_810,
Mus musculus	ENSMUSG00000074129	3 retrocopies	retro_mmus_1129, retro_mmus_1334, retro_mmus_20,
Oryctolagus cuniculus	ENSOCUG00000025258	9 retrocopies	retro_ocun_1038, retro_ocun_1077, retro_ocun_1392, retro_ocun_1462, retro_ocun_304, retro_ocun_674, retro_ocun_756, retro_ocun_786, retro_ocun_972,
Pteropus vampyrus	ENSPVAG00000010958	3 retrocopies	retro_pvam_129, retro_pvam_625, retro_pvam_771,
Rattus norvegicus	ENSRNOG00000020618	10 retrocopies	retro_rnor_1073, retro_rnor_1112, retro_rnor_1212, retro_rnor_1292, retro_rnor_1357, retro_rnor_1742, retro_rnor_564, retro_rnor_593, retro_rnor_665, retro_rnor_988,
Sus scrofa	ENSSSCG00000003166	4 retrocopies	retro_sscr_290, retro_sscr_300, retro_sscr_392, retro_sscr_743,