RetrogeneDB ID: retro_amel_1034

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192847.1:1118347..1118549(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED10
• Ensembl ID: ENSAMEG00000006767
• Aliases: None
• Description: mediator complex subunit 10 [Source:HGNC Symbol;Acc:28760]

Sequence

>retro_amel_1034
ACTGATTTACAGATGATTGATAATGCAGACAGCAGCTTCATAATATTACTCACCTTCAGCAGTTCTTCAATCTATAGATC
CAGACTGAAACTCCCAACCTTATATGGAAACATGCTTAGAGATGTCTCTAGCTAAAAATGAATAAGCTAAAGGCAAAATT
GACACAAAAAAGAAATTTTAAACCCTTCTGCTTCAAGAACTG

Alignment

ORF - retro_amel_1034 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.0 %
• Parental protein coverage: 72.34 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TGLQDIDK-CRQQLHDIT-VPLEVFEYIDQGRNPQLYTKECLERALAKNEQVKGKIDTMKKFKSLLIQEL
          T.LQ.ID..CRQQLH.IT..P..V...ID...N.Q.Y...CLE..LAKNE..KGKIDT.KKF..LL.QEL
Retrocopy TDLQMIDN<CRQQLHNIT<SPSAVLQSIDPD*NSQPYMETCLEMSLAKNE*AKGKIDTKKKF*TLLLQEL

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_1034 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1034 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	ENSAMEG00000006767	1 retrocopy	retro_amel_1034 ,
Canis familiaris	ENSCAFG00000010346	1 retrocopy	retro_cfam_721,
Dasypus novemcinctus	ENSDNOG00000004579	1 retrocopy	retro_dnov_1286,
Equus caballus	ENSECAG00000023738	1 retrocopy	retro_ecab_796,
Echinops telfairi	ENSETEG00000000027	1 retrocopy	retro_etel_1758,
Monodelphis domestica	ENSMODG00000002025	1 retrocopy	retro_mdom_399,
Otolemur garnettii	ENSOGAG00000005988	1 retrocopy	retro_ogar_1830,
Ochotona princeps	ENSOPRG00000015506	1 retrocopy	retro_opri_834,
Tupaia belangeri	ENSTBEG00000014579	2 retrocopies	retro_tbel_1647, retro_tbel_4561,
Tarsius syrichta	ENSTSYG00000002763	1 retrocopy	retro_tsyr_792,