RetrogeneDB ID: retro_amel_1501

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193514.1:263389..263895(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000017710
• Aliases: None
• Description: None

Sequence

>retro_amel_1501
TTCAAAATAGAGGTTGTTATGGTGACAGACTATGAAGCTTTTATCAAAATCCCAGGCTGTCAGAAGCAGGGTCTGGTCCG
TCGAACTCACATGTGATCCTGTTGCATGGATAAGCCCTCTGAGATAGTAGATGTCAGAGAAAAGGTGTGGGTGAAACTTA
TTGGCTTATAGATGAAAAATGATAAGATAAAAGTATCCTTCTCCATAAAAGTTGTCAACCATGGGACTGAGAAAGACCTT
GCCCCCAACAATGTTATCACTGGGCAAGAAGACAGGCAGAGGCAGTCCTTCCATGATTACACTGGGAAGATCACCCTCAA
AGCTATCCTGTACACCACCTACAAGGTGTGTGTTGATAGAGACCACTTTGCAAAGGGTTGTTTTATGCAACCATGAGGAA
CTAAATATTCTCTGATACCTAATGAGGAAGAGGAGAAGGAAGAGGAAAATAAGCAGAGTTTGAGAAGCGTGACCCAGTGA
GGAATTCTTCTAGAAAAAGAAAGAAG

Alignment

ORF - retro_amel_1501 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.27 %
• Parental protein coverage: 70.54 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSLSMK
          F..EV.MVTDY.AFIKIPGC.KQGLV.RTHM.SC..DKPSEIVDV..KVWVKLIG..MKND.IKVS.S.K
Retrocopy FKIEVVMVTDYEAFIKIPGCQKQGLVRRTHM*SCCMDKPSEIVDVREKVWVKLIGL*MKNDKIKVSFSIK

Parental  VVNQGTGKDLDPNNVIIEQEERRRRSFQDYTGQKITLEAVLNTTCKKCGCKGHFAKDCFMQPGGTKYSLI
          VVN.GT.KDL.PNNVI..QE.R.R.SF.DYTG.KITL.A.L.TT.K.C....HFAK.CFMQP.GTKYSLI
Retrocopy VVNHGTEKDLAPNNVITGQEDRQRQSFHDYTG-KITLKAILYTTYKVCVDRDHFAKGCFMQP*GTKYSLI

Parental  PDEEEEKEE-AKSAEFEKPDPTKNSSRKRKK
          P.EEEEKEE..K.AEFEK.DP..NSSRKRKK
Retrocopy PNEEEEKEE<GK*AEFEKRDPVRNSSRKRKK

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_1501 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1501 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 16 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017710	1 retrocopy	retro_amel_1501 ,
Bos taurus	ENSBTAG00000016818	2 retrocopies	retro_btau_168, retro_btau_273,
Canis familiaris	ENSCAFG00000011131	2 retrocopies	retro_cfam_485, retro_cfam_835,
Callithrix jacchus	ENSCJAG00000006259	1 retrocopy	retro_cjac_4218,
Dasypus novemcinctus	ENSDNOG00000000509	1 retrocopy	retro_dnov_2548,
Dipodomys ordii	ENSDORG00000004128	1 retrocopy	retro_dord_200,
Echinops telfairi	ENSETEG00000007421	1 retrocopy	retro_etel_1280,
Loxodonta africana	ENSLAFG00000015364	1 retrocopy	retro_lafr_534,
Myotis lucifugus	ENSMLUG00000000594	1 retrocopy	retro_mluc_2176,
Monodelphis domestica	ENSMODG00000017082	1 retrocopy	retro_mdom_252,
Mustela putorius furo	ENSMPUG00000015442	1 retrocopy	retro_mputfur_680,
Mus musculus	ENSMUSG00000028772	1 retrocopy	retro_mmus_2150,
Otolemur garnettii	ENSOGAG00000013749	1 retrocopy	retro_ogar_1225,
Sorex araneus	ENSSARG00000007944	1 retrocopy	retro_sara_691,
Ictidomys tridecemlineatus	ENSSTOG00000003825	1 retrocopy	retro_itri_405,
Tursiops truncatus	ENSTTRG00000014870	2 retrocopies	retro_ttru_1383, retro_ttru_1613,