RetrogeneDB ID: retro_amel_1924

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL199511.1:478..884(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000013753
• Aliases: None
• Description: None

Sequence

>retro_amel_1924
AGTCTGGAGACCATCAATGAAGGGAAGACGGGTGAGCTACAAAACTATAACAAGTACAAATCTGTATTATTGAAGAATGG
ATGGGACCCTGGGGAAGAGGGACCGGACATGGCTCGCCGGAATCTCCTGATGCTGGTAGACTGTCCCCTGAACCAGACTG
TGTTGCTTCAGATTACATACACACACGGAGGAATGTGCGGGCTGAAGTGAACAGCCAGACTTGAATTCCAGGAACCCTTA
CATCGCATTTGTAACCTCAGGGTTCAGCTCTTACATACACTCACTCATTGTCCAAACAGATCATGGCCCCAAGAAGCTTT
TGAAGATACTTAATCCAGTGTGAGATCAAAACCCATTTGAATGTATGAAAATTGACACGTCCTTCTCCATCCCAGTGATC
TGTGAG

Alignment

ORF - retro_amel_1924 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.97 %
• Parental protein coverage: 55.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SLETVKVGKTYELLNCDKHKSVLLKNGRDPGEVRPDIAHQSLLMLMDSPLNRAGLLQV-YIHTQKNVLIE
          SLET...GKT.EL.N..K.KSVLLKNG.DPGE..PD.A...LLML.D.PLN...LLQ..YIHT..NV..E
Retrocopy SLETINEGKTGELQNYNKYKSVLLKNGWDPGEEGPDMARRNLLMLVDCPLNQTVLLQI<YIHTRRNVRAE

Parental  VNPQTRIPRT-FERFCGLMVQLLHKLS-VRAADGPQKLLKVIKNPVSDHFPVGCMKIGTSFSIPVVSD
          VN.QT.IP.T...R.C.L.VQLLH.L......D...K.L..I.NPV.D..P..CMKI.TSFSIPV...
Retrocopy VNSQT*IPGT>LHRICNLRVQLLHTLT>IVQTDHGPKKLLKILNPV*DQNPFECMKIDTSFSIPVICE

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_1924 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1924 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013753	1 retrocopy	retro_amel_1924 ,
Callithrix jacchus	ENSCJAG00000007120	1 retrocopy	retro_cjac_2960,
Gorilla gorilla	ENSGGOG00000004287	1 retrocopy	retro_ggor_3077,
Macropus eugenii	ENSMEUG00000000831	1 retrocopy	retro_meug_1299,
Myotis lucifugus	ENSMLUG00000009196	1 retrocopy	retro_mluc_737,
Macaca mulatta	ENSMMUG00000010207	1 retrocopy	retro_mmul_671,
Nomascus leucogenys	ENSNLEG00000005080	1 retrocopy	retro_nleu_501,
Otolemur garnettii	ENSOGAG00000006975	2 retrocopies	retro_ogar_2971, retro_ogar_945,
Pongo abelii	ENSPPYG00000004215	1 retrocopy	retro_pabe_2924,
Rattus norvegicus	ENSRNOG00000012828	1 retrocopy	retro_rnor_1459,