RetrogeneDB ID: retro_amel_1818

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194579.1:61572..61841(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM230
• Ensembl ID: ENSAMEG00000009083
• Aliases: None
• Description: transmembrane protein 230 [Source:HGNC Symbol;Acc:15876]

Sequence

>retro_amel_1818
ATGCCCTCCCGAACCAGCCTGGCTGCTGGAATCCCCAGTAGTAAAGCGAAATGCTTAAGGCTCTCCAGTACAGACTAGGG
CTACATTGACTTTCAGTTTAAAAAAAGCCCTCCTAAGATCACACAGAGGCCTCTGTGCTTGCTAGCGTGTGCTGGCTCTG
AATGGCGCCTTTCTCATTTTCATAGGCGTCCCCCGCCCCAGCAGGCAGGCAAGGAGGGGGTGCAAACAGGTGGGGCCTAT
CCATCCCCATCCTTGATGTCCTGATCTTT

Alignment

ORF - retro_amel_1818 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.95 %
• Parental protein coverage: 71.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPSRTNLATGIPSSKVKYSRLSSTGDGYIDLQFKKSPPKIPYKAIALAT-VLFLIGAFLIIIG-SLLLAG
          MPSRT.LA.GIPSSK.K..RLSST..GYID.QFKKSPPKI......L...VL.L.GAFLI.IG.S...AG
Retrocopy MPSRTSLAAGIPSSKAKCLRLSSTD*GYIDFQFKKSPPKITQRPLCLLA>VLALNGAFLIFIG>SPAPAG

Parental  YISKGGADRAVPVLIVGILVF
          ....G.........I...L.F
Retrocopy RQGGGANRWGLSIPILDVLIF

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_1818 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1818 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 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009083	1 retrocopy	retro_amel_1818 ,
Bos taurus	ENSBTAG00000006063	2 retrocopies	retro_btau_1079, retro_btau_147,
Dasypus novemcinctus	ENSDNOG00000005724	5 retrocopies	retro_dnov_1004, retro_dnov_2377, retro_dnov_2534, retro_dnov_373, retro_dnov_803,
Myotis lucifugus	ENSMLUG00000023089	2 retrocopies	retro_mluc_1504, retro_mluc_1759,
Ochotona princeps	ENSOPRG00000008611	1 retrocopy	retro_opri_502,
Ictidomys tridecemlineatus	ENSSTOG00000019378	1 retrocopy	retro_itri_35,