RetrogeneDB ID: retro_amel_16

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192597.1:219856..221188(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000018816
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: BECN1
• Ensembl ID: ENSAMEG00000006867
• Aliases: None
• Description: None

Sequence

>retro_amel_16
CTTGGAATTAGAGTGAGAGCCAAGGCCTCTACCATGTCCTTCACCCGCTTCATTTGCCAGGGCTGCAGGCAGCCCATGAA
GCTGGATCAGTCCACGGGGACCTTGGGTCTCGAGAGCACCCAAGAATCTGCAGCTTCCACATTCGCCTCAGCTCAGAAGG
AGCCAGGAGAAACCCTGCAGCGTGGCCCTCCCTCCAAGGTGGAGACGGACAGTGAGAAGCTGCAAGATGGTGCCTCCTGT
TCTACCCTCCCTGGCAATGGCAAGATGTCAAGAGACAGTTCTAACAAGTTCATCTTGCTTGGAAAGTTTGACTCAGCAAG
AACGCTCAGTAACATCCAGAAGACTGCGAGGGACATTTTTGACATCCTCACTGGTGAAGAAGATATGGACCGCCCCCTAT
GTGAGGACTGTACCGACGAACTTTTAGAACAAGTGGACACCCAGCTCATTATTGTAGAATCTGAGAACCAGAAGTACAAA
TATTGGATGGGGAGGATACGTGAGGAGGAGAAGAAGACATTGCAGGGGGAGTTGGAGGGCCTGGAGCTGGAGGAGGCGAC
GCTGATGCAGGAGCTGAAGGAGGTGGAGAAGAACCGAGAAAGAATAGCAGCAGATCTGGAGGCCGCCCGGGCAGAGACGA
AGGCGCTCGACCAGCAGAACGAGCAGTACTGGAGGGATTATAGTAACTTGCAATGGCAGCAACTGGAACTGCAGGACCAG
CTGAGGAGCATAAAGCACCAGCTGAGATATGCCCAGATCCAGTGGGGCCGGCTGACGAAGACCAACGTCTTCAATGCCAC
CTTTGAGATCAGGCATGATGGCCCTGTGGGCATCATCAATAGCTTCAGATTGGGCTGCCTCCCCACCATCCCCGTGAGCT
GGAAGGAGATTAACATGGCCTGGGGCCAGACAGCCTTGCTGCTCCTTGCCCTGTCCAACAAAATTGGGCTGGAGTTTCAG
AGGTATCGACTAGTCCCCTGTGGAGAGCGGTCCTGTCTGAAGTCTGTAACGGCTGACCCCGTTGAGCTGCCGCTGTTCTA
CACCGCGGGGCAGAGAACTTGCTTGCATGTCAAATTTGACCAGGCAATGATGGCTTTTTTGGACTGCATGCAGCAGTTCA
AGGAAGAGGCTGAGAAAGGCAAGGGGGGTCTTTGCCTGCCCTGCAGGATTCATGTGGAGAGTGGCGTAATGGAAGACTCT
AGAAGCAGTGGTGAGTTCTATTCCATCAGAACCCACTTGAACACAGAGGAGCAGTGGACAAAGGCACTCAGGCTCATGCT
TATAAATTTTAGGCATAGTCTCGATTGGGTCTCTTTAAGATATCAAGAATAG

Alignment

ORF - retro_amel_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.32 %
• Parental protein coverage: 61.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QMSEDDSEQLQLELKELVLEEGRLIQELEDVEKNRKIVAENLEKVQAEAERLDQEEAQYQREYSEFKRQQ
          ...E.....LQ.EL..L.LEE..L.QEL..VEKNR...A..LE...AE...LDQ...QY.R.YS....QQ
Retrocopy RIREEEKKTLQGELEGLELEEATLMQELKEVEKNRERIAADLEAARAETKALDQQNEQYWRDYSNLQWQQ

Parental  LELDDELKSVENQMRYAQMQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEWNEINAAWGQT
          LEL.D.L.S...Q.RYAQ.Q...L.KTNVFNATF.I.H.G..G.IN.FRLG.LP..PV.W.EIN.AWGQT
Retrocopy LELQDQLRSIKHQLRYAQIQWGRLTKTNVFNATFEIRHDGPVGIINSFRLGCLPTIPVSWKEINMAWGQT

Parental  VLLLHALANKMGLKFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFFWDNKFDHAMVAFLDCVQQFK
          .LLL.AL.NK.GL.FQRYRLVP.G..S.L.S.T....ELPL....G.R.....KFD.AM.AFLDC.QQFK
Retrocopy ALLLLALSNKIGLEFQRYRLVPCGERSCLKSVTADPVELPLFYTAGQRTCLHVKFDQAMMAFLDCMQQFK

Parental  EEVEKGETRFCLPYRMDVEKGKIEDTGGSGGSYSIKTQFNSEEQWTKALKFMLTNLKWGLAWVSSQF
          EE.EKG....CLP.R..VE.G..ED...SG..YSI.T..N.EEQWTKAL..ML.N....L.WVS...
Retrocopy EEAEKGKGGLCLPCRIHVESGVMEDSRSSGEFYSIRTHLNTEEQWTKALRLMLINFRHSLDWVSLRY

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_16 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_16 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 17 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006867	1 retrocopy	retro_amel_16 ,
Bos taurus	ENSBTAG00000019914	1 retrocopy	retro_btau_226,
Dipodomys ordii	ENSDORG00000000956	1 retrocopy	retro_dord_675,
Felis catus	ENSFCAG00000013136	1 retrocopy	retro_fcat_62,
Homo sapiens	ENSG00000126581	1 retrocopy	retro_hsap_335,
Macropus eugenii	ENSMEUG00000011700	1 retrocopy	retro_meug_600,
Macaca mulatta	ENSMMUG00000029971	1 retrocopy	retro_mmul_81,
Monodelphis domestica	ENSMODG00000015064	1 retrocopy	retro_mdom_1778,
Mus musculus	ENSMUSG00000035086	1 retrocopy	retro_mmus_390,
Nomascus leucogenys	ENSNLEG00000011840	1 retrocopy	retro_nleu_1776,
Oryctolagus cuniculus	ENSOCUG00000015964	3 retrocopies	retro_ocun_1021, retro_ocun_1732, retro_ocun_218,
Procavia capensis	ENSPCAG00000014049	1 retrocopy	retro_pcap_345,
Pan troglodytes	ENSPTRG00000022819	1 retrocopy	retro_ptro_268,
Sorex araneus	ENSSARG00000000367	1 retrocopy	retro_sara_136,
Sus scrofa	ENSSSCG00000017386	1 retrocopy	retro_sscr_75,
Ictidomys tridecemlineatus	ENSSTOG00000012612	1 retrocopy	retro_itri_25,
Tursiops truncatus	ENSTTRG00000011716	1 retrocopy	retro_ttru_595,