RetrogeneDB ID: retro_amel_1880

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL195140.1:19451..20101(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KHDC3L
• Ensembl ID: ENSAMEG00000007887
• Aliases: None
• Description: KH domain containing 3-like, subcortical maternal complex member [Source:HGNC Symbol;Acc:33699]

Sequence

>retro_amel_1880
AGGCGGTTTCTGACACTTGTGAGCTGGAGAAGCAAGAAGGGACGCTATTCACAGTGCTCCTTAACCTCAGCAAGCGGCCC
TACTGGTTCCACTCCCAGTATCTGAAGAGTCCAAAGGCAGTTCATCTTGAGGTGTGGCTGGTGGAAGCGAAATTCCACCT
GGGAGGAGAGCACATCCCGCAGGTCGAGTGGTGTCGCAGACCCTACTTCATGTTAATCAGCGGGACCCCAAGGGCGAAGC
TGAGATATTTGGTCGGCCTTATTACCAGAAAGATGTAGCCAAGATGATCATGAATTTGGCTGACTATCACTGCCAACTCT
GGGTACAAAGCTCAGAGGAGGTCCCTGCCCAGAACGCATCCACCCAGTGGCCCCCCCGGTGCATCCCACGAGGCGGTGAC
CCAGCGGTCCCCCGGCGCAGCCCGGGAGGCGGGGACACAGAGCTCCCCCGGTGCAGCCCAGGAGCCAAGGACACAGAGCT
CCCCCTGCGCAGCCCGGGAGGCAGCGACACAGCGGTCCCCAGGCACAGCCGGAGAGGCGGCCACCCAGCGGTTCCCCGGC
GCAGCCCGCAAGGCGGGGACACAGAGCTCAACCCGTGCATCCCGGGAGGCGGCGACCCAGAGCTCCCCCCCCCGCACAGC
ACACGAGGTG

Alignment

ORF - retro_amel_1880 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.42 %
• Parental protein coverage: 96.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KRFPTLV-QLEQREGTLFTVLGNLSKRPYWFHSEYLKSPKAVHLEAWLVEAIFGRGGEHIPHVE-CVSQT
          .RF.TLV..LE..EGTLFTVL.NLSKRPYWFHS.YLKSPKAVHLE.WLVEA.F..GGEHIP.VE..VSQT
Retrocopy RRFLTLV<ELEKQEGTLFTVLLNLSKRPYWFHSQYLKSPKAVHLEVWLVEAKFHLGGEHIPQVE<VVSQT

Parental  LLHVNQWDPEGEAEILIFGRPYYQKDVAKMIMNLADYHRQLRAQSSEEVPAQDASTQRSPE-AAREAETQ
          LLHVNQ.DP.GEAE..IFGRPYYQKDVAKMIMNLADYH.QL..QSSEEVPAQ.ASTQ..P..A..EA.TQ
Retrocopy LLHVNQRDPKGEAE--IFGRPYYQKDVAKMIMNLADYHCQLWVQSSEEVPAQNASTQWPPR>ASHEAVTQ

Parental  RSPEAAREAATQSSPKAAREATTQRSP-KAREAATQRSPGAAREAATQSSLGAARETVTQRSPDAVREAA
          RSP.AAREA.TQSSP.AA.E..TQ.SP..AREAATQRSPG.A.EAATQ...GAAR...TQ.S..A.REAA
Retrocopy RSPGAAREAGTQSSPGAAQEPRTQSSPCAAREAATQRSPGTAGEAATQRFPGAARKAGTQSSTRASREAA

Parental  TQRSPDATQDPV
          TQ.....T...V
Retrocopy TQSXXXXTAHEV

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_1880 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1880 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007887	1 retrocopy	retro_amel_1880 ,
Callithrix jacchus	ENSCJAG00000009947	1 retrocopy	retro_cjac_1153,
Myotis lucifugus	ENSMLUG00000004469	1 retrocopy	retro_mluc_2196,
Ochotona princeps	ENSOPRG00000013565	3 retrocopies	retro_opri_322, retro_opri_406, retro_opri_651,
Sorex araneus	ENSSARG00000003714	1 retrocopy	retro_sara_631,