RetrogeneDB ID: retro_amel_1110

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192913.1:79373..79768(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OSTC
• Ensembl ID: ENSAMEG00000001753
• Aliases: None
• Description: oligosaccharyltransferase complex subunit (non-catalytic) [Source:HGNC Symbol;Acc:24448]

Sequence

>retro_amel_1110
CTTGGCCTCGATTGTCCCGACCTGAGGCTGAGAAGTCACCCGGGGTGCCGGGTGATGATTGTGTAGGCGCTGGAGGTGGG
GTCTGGTTTCCTCATCAGGGGAGGGACACTGATGATGTGGTTGCCCAACTTCCAAGTGTCGGCTCTGTGTCTGATGAATG
TGGCTGTCAGAGGCCAGCAGCTTTCGTGGCCTACAGAGTAAATGGACAAGATATTGAAGGATTTGCATCCAGCTTCCTGT
TTACAGTGGGAAGTTGGGAGCTTCTGTTTCATAAGCCTGGACCAAGCAATGCACCCAACGTTCCAAAATGCAGTAGATTT
CTTCTGTTCATTGGACTCATCTGTGTCCGGTTGGTTTCTTTCATGGCTAGGCCGTTCGTGACTATGAACCTGCCA

Alignment

ORF - retro_amel_1110 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.43 %
• Parental protein coverage: 90.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LVLECPNLKLKKPPWVHMPSAMTVYALVVVSYFLITGGIIY-DVIVEPPSVGSMTDEHGHQRPVAFLAYR
          L.L.CP.L.L...P.......M.V.AL.V.S.FLI.GG....DV....PSVGS..DE.G.QRP.AF.AYR
Retrocopy LGLDCPDLRLRSHPGCRV---MIV*ALEVGSGFLIRGGTLM<DVVAQLPSVGSVSDECGCQRPAAFVAYR

Parental  VNGQYIMEGLASSFLFTMGGLGFIILDRSNAPNIP---KLNRFLLLFIGFVCVLLSFFMASRVFKRMKLP
          VNGQ.I.EG.ASSFLFT.G.............N.P...K..RF.LLFIG..CV.L..FMA.R.F..M.LP
Retrocopy VNGQDI-EGFASSFLFTVGSWE-LLFHKPGPSNAPNVPKCSRF-LLFIGLICVRLVSFMA-RPFVTMNLP

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_1110 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1110 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 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001753	2 retrocopies	retro_amel_1110 , retro_amel_165,
Canis familiaris	ENSCAFG00000011286	12 retrocopies	retro_cfam_1129, retro_cfam_1206, retro_cfam_1459, retro_cfam_1462, retro_cfam_1575, retro_cfam_1851, retro_cfam_1910, retro_cfam_1948, retro_cfam_2003, retro_cfam_263, retro_cfam_296, retro_cfam_814,
Callithrix jacchus	ENSCJAG00000016002	3 retrocopies	retro_cjac_121, retro_cjac_2981, retro_cjac_324,
Cavia porcellus	ENSCPOG00000024467	1 retrocopy	retro_cpor_659,
Echinops telfairi	ENSETEG00000003717	4 retrocopies	retro_etel_1564, retro_etel_492, retro_etel_878, retro_etel_970,
Gorilla gorilla	ENSGGOG00000026873	6 retrocopies	retro_ggor_1457, retro_ggor_2060, retro_ggor_215, retro_ggor_2427, retro_ggor_370, retro_ggor_385,
Monodelphis domestica	ENSMODG00000020599	1 retrocopy	retro_mdom_428,
Mustela putorius furo	ENSMPUG00000008869	1 retrocopy	retro_mputfur_1451,
Mus musculus	ENSMUSG00000041084	1 retrocopy	retro_mmus_648,
Oryctolagus cuniculus	ENSOCUG00000011056	2 retrocopies	retro_ocun_1318, retro_ocun_7,
Pteropus vampyrus	ENSPVAG00000005915	1 retrocopy	retro_pvam_924,
Rattus norvegicus	ENSRNOG00000023322	1 retrocopy	retro_rnor_2297,
Sus scrofa	ENSSSCG00000009145	1 retrocopy	retro_sscr_503,
Ictidomys tridecemlineatus	ENSSTOG00000021644	6 retrocopies	retro_itri_1211, retro_itri_1386, retro_itri_15, retro_itri_1571, retro_itri_789, retro_itri_863,
Tarsius syrichta	ENSTSYG00000000724	2 retrocopies	retro_tsyr_1193, retro_tsyr_921,