RetrogeneDB ID: retro_amel_1882

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL195148.1:22084..22686(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED4
• Ensembl ID: ENSAMEG00000003718
• Aliases: None
• Description: mediator complex subunit 4 [Source:HGNC Symbol;Acc:17903]

Sequence

>retro_amel_1882
GAGGTCTTGTCAAGAGAACTTATAGAAATGCTAGCAATTTCAAGAAACCAAATGTTGTTGCCGTCAGATGAGGAGAACTA
GGTCCCGGAATTGTTAATATCCAGAGATGGGGAATTTCAAGAACTGATGAAATTGGCACTCAATCAGGGAAATACCCATC
ATGAAATGTAAGCTGTAGAAAAGGAAGTGGAGAAGAGAGATAGTGATATTCACTAACTACAAAAATGCTAAAGGAAGCAG
AACAAATACTGGCCACAGTGTTTACCAAGCAAAAGAAAAACTCAAATCAGTAGAAAAAGCAAGACAAGGTACCATCTCCT
CCAAAGAAATAATTAAGTATGCACATAGGATTAGTGCAAGTAATGCAGCGTGTGCCCCACTGACCTAGGTCCCAGGGGAC
CTATGGTGACCACATCCAACTGATTAGAGCTGAGAAGTGGATTACCGGGTCAAATGAATAATCCTTCCACTAATGGTATA
AATGGTCATTATCAGGGGATGTCCTCACAGCAGGCAGATTGCCAGATGTCCTTGCTCCACAATACCCATCGCAGTCAAGT
GACATGGCAATGAATACGCTACCACCAAATCACGGGAATGAC

Alignment

ORF - retro_amel_1882 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.13 %
• Parental protein coverage: 74.81 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EVLSRELIEMLAISRNQKLLPPDEENQVLELLIHRDGGFQERMKLARNRGKIHHEMQVLEKEVEKRDSDI
          EVLSRELIEMLAISRNQ.LLP.DEEN.V.ELLI.RDG.FQE.MKLA.N.G..HHEM...EKEVEKRDSDI
Retrocopy EVLSRELIEMLAISRNQMLLPSDEEN*VPELLISRDGEFQELMKLALNQGNTHHEM*AVEKEVEKRDSDI

Parental  QQLQ-KQLKEAEQILAT-AVYQAKEKLKSIEKARKGAISSEEIIKYAHRISASNAVCAPLTWVPGDPRRP
          ..LQ.K.LKEAEQILAT..VYQAKEKLKS.EKAR.G.ISS.EIIKYAHRISASNA.CAPLT.VPGD...P
Retrocopy H*LQ<KMLKEAEQILAT<SVYQAKEKLKSVEKARQGTISSKEIIKYAHRISASNAACAPLT*VPGDLW*P

Parental  YPTD-LEMRSGLLGQMNNPSTNGVNGH-LPGDALAAGRLPDVLAPQYPWQSNDMSMNMLPPNHSND
          .PTD.LE.RSGL.GQMNNPSTNG.NGH.L.GD.L.AGRLPDVLAPQYP.QS.DM.MN.LPPNH.ND
Retrocopy HPTD<LELRSGLPGQMNNPSTNGINGH<LSGDVLTAGRLPDVLAPQYPSQSSDMAMNTLPPNHGND

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_1882 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1882 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003718	1 retrocopy	retro_amel_1882 ,
Canis familiaris	ENSCAFG00000004451	1 retrocopy	retro_cfam_1792,
Callithrix jacchus	ENSCJAG00000009256	1 retrocopy	retro_cjac_3937,
Dasypus novemcinctus	ENSDNOG00000018064	1 retrocopy	retro_dnov_1342,
Myotis lucifugus	ENSMLUG00000009265	1 retrocopy	retro_mluc_178,
Mustela putorius furo	ENSMPUG00000001437	1 retrocopy	retro_mputfur_162,
Mus musculus	ENSMUSG00000022109	1 retrocopy	retro_mmus_3576,
Sorex araneus	ENSSARG00000001473	1 retrocopy	retro_sara_353,
Tupaia belangeri	ENSTBEG00000014259	1 retrocopy	retro_tbel_292,