RetrogeneDB ID: retro_amel_47

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193482.1:153157..154945(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000019937
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000014293
• Aliases: None
• Description: None

Sequence

>retro_amel_47
ATGTCTGACAACGGGAGCAGCACAGATGGCCCACAAGACTCAGGAAAAAGAAGCCCGCTCAATAGTCCTGAGGAGCAGTC
TGACGTGGATGTCAGGAGAGAGACCTCCTCAGACACTGAACTGAGCTTGAATCTGACCAGAGATGGTGGCGTCCTCAGCC
AGGCCACCCCAGAAAGTCAAGGCACAGACGTAGAAGGTTCAGCTGAAAACATCAACTTTGAAAGCACGGAAGATTCTGAC
CAGTTCTTCATCTGTGAGGAAAACTTATTCGCTTACCGCGCAGCAGGAGAGGAGGAGCTAGGAGCGGAAGAGGGGGCGAG
AGGAGCGGCAGAAGAGCAGCCTCAGGTACAGTGCGATGAAGCTAACCGCGATCAGTATTTATCAGAAGGGGATCGGGCCC
TGGAGGACTGGGTGTCCTCTGAAACATCTGCCCTGCCCCGCCCTCGCTGGCAAGTCCTTTCCGCTCTTCGAGAGCGGCAG
CTGGGTTCCAGTGCCCGCTTCGTGTATGAGGCCTGTGGGGCAAGAGTTTTTGTGCAGCGTTTCCAGCTGCTCTGTGAGCT
TGAAGGCCATCACGGCTGTGTCAATACTGTGCACTTTAACCAGCGTGGCACCTGGCTGGCCAGTAGCAGTGATGACCTTA
AAGTGATAGTGTGGGACTGGGTGCGTCAGCACCCAGTACTGGAGTTTGCGAGTGGCCACAAAAATAATGTCTTTCAAGCC
AAGTTCCTTCCCAATTGTGGTGATTCCACCTTGGCCATGTGTGCCCGTGATGGGCAGATACGCATAGCAAAGCTCTCTGC
TCTACCACACTGTAAGAATACTAAGCTTGTGGCCCAGCACAGGGGAGCCTCCCATAAGTTGGCTCTGGAGCCAGACTCCC
CTTTTAAGTTCCTAACTTCAGGTGAAGATGCAGTTGTTTTCGCCATTGATCTCAGACAAGACCAGCCAGCTTCCAGAGTG
GTGGTAACCAAAGAGGGGGAGAAGAAAGTGGGGCTGTATACGATCCATGTGAATCCTGCCAATACTTACCAGTTTGCAGT
GGGCGGAAGAGATCAGTTTGTAAGAATTTATGACCAGAGGAAAATTAATGAGAATGAGAATAATGGGGTACTCAAGAAAT
TCTGTCCTCATCATCTAGTCAACTGTGATTCCAAAGTAAACATCACCTGCCTCGTTTACAGTCACGATGGCACAGAGCTC
CTGGCCAGTTACAATGATGAAGATATTTATCTCTTCAACTCCTCTGATGGAGATGGAGCCCAGTATGTTAAGAGATACAA
GGGGCACAGAAATAGTGCCACAATCAAAGGTGTCAATTTCTATGGTCCCAGAAGTGAGTTTGTGGTGAGCGGCAGTGATT
GTGGGCACATCTTCCTCTGGGAAAAATCATCCTGCCAGATCGTTCAGTTCATGGAGGGGGACAAGGGAGGCACCATAAAC
TGCCTTGAGCCCCATCCTTACCTACCTGTGCTGGCTACCAGTGGCCTAGATCATGATGCCAAGATCTGGGCACCCACAGC
TAAAGCTGCCACTGATCTGGCTGGGTTAAAGAATATGATTAAGACAAACAAGAGAGAACGAGATGAAGATCGCATACACC
GCACTGACCTGTTCGACAGCCACATGCTTTGGTTCCTCATGCGTCACCTGACACAGAGAGGTCATCACCAGCGCTGGGGA
GCTCCTGGAGTTGGAGTCATGGATGCAGAGTCAAATGCGTCTTCCAGTACCTCCAATTCATCTGAGGAGGAAGAGAACCA
AGACCGTGTGCAGTGCCTGCCATCCTGA

Alignment

ORF - retro_amel_47 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.4 %
• Parental protein coverage: 66.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEEEEEEEEEHPRRRVQRKRANRDQDSSDDERALEDWVSSETSALPRPRWQALPALRERELGSSARFVYE
          EE......EE.P...VQ...ANRDQ..S...RALEDWVSSETSALPRPRWQ.L.ALRER.LGSSARFVYE
Retrocopy EEGARGAAEEQPQ--VQCDEANRDQYLSEGDRALEDWVSSETSALPRPRWQVLSALRERQLGSSARFVYE

Parental  ACGARVFVQRFRLQHGLEGHTGCVNTLHFNQRGTWLASGSDDLKVVVWDWVRRQPVLDFESGHKSNVFQA
          ACGARVFVQRF.L...LEGH.GCVNT.HFNQRGTWLAS.SDDLKV.VWDWVR..PVL.F.SGHK.NVFQA
Retrocopy ACGARVFVQRFQLLCELEGHHGCVNTVHFNQRGTWLASSSDDLKVIVWDWVRQHPVLEFASGHKNNVFQA

Parental  KFLPNSGDSTLAMCARDGQVRVAELSATQCCKNTKRVAQHKGASHKLALEPDSPCTFLSAGEDAVVFTID
          KFLPN.GDSTLAMCARDGQ.R.A.LSA...CKNTK.VAQH.GASHKLALEPDSP..FL..GEDAVVF.ID
Retrocopy KFLPNCGDSTLAMCARDGQIRIAKLSALPHCKNTKLVAQHRGASHKLALEPDSPFKFLTSGEDAVVFAID

Parental  LRQDRPASKLVVTKEKEKKVGLYTIFVNPANTHQFAVGGRDQFVRIYDQRKIDENENNGVLKKFCPHHLV
          LRQD.PAS..VVTKE.EKKVGLYTI.VNPANT.QFAVGGRDQFVRIYDQRKI.ENENNGVLKKFCPHHLV
Retrocopy LRQDQPASRVVVTKEGEKKVGLYTIHVNPANTYQFAVGGRDQFVRIYDQRKINENENNGVLKKFCPHHLV

Parental  NSESKANITCLVYSHDGTELLASYNDEDIYLFNSSHSDGAQYVKRYKGHRNNATVKGVNFYGPKSEFVVS
          N..SK.NITCLVYSHDGTELLASYNDEDIYLFNSS..DGAQYVKRYKGHRN.AT.KGVNFYGP.SEFVVS
Retrocopy NCDSKVNITCLVYSHDGTELLASYNDEDIYLFNSSDGDGAQYVKRYKGHRNSATIKGVNFYGPRSEFVVS

Parental  GSDCGHIFLWEKSSCQIVQFMEGDKGGVVNCLEPHPHLPVLATSGLDHDVKIWAPTAETSTELTGLKDVI
          GSDCGHIFLWEKSSCQIVQFMEGDKGG..NCLEPHP.LPVLATSGLDHD.KIWAPTA...T.L.GLK..I
Retrocopy GSDCGHIFLWEKSSCQIVQFMEGDKGGTINCLEPHPYLPVLATSGLDHDAKIWAPTAKAATDLAGLKNMI

Parental  KKNKRERDEDSLHHTDLFDSHMLWFLMHHLRQRRHHRRWREPGVGATDADSDESPSSSDTSDEEEGPDRV
          K.NKRERDED..H.TDLFDSHMLWFLM.HL.QR.HH.RW..PGVG..DA.S..S.S.S..S.EEE..DRV
Retrocopy KTNKRERDEDRIHRTDLFDSHMLWFLMRHLTQRGHHQRWGAPGVGVMDAESNASSSTSNSSEEEENQDRV

Parental  QCMPS
          QC.PS
Retrocopy QCLPS

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_47 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_47 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 12 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014293	1 retrocopy	retro_amel_47 ,
Bos taurus	ENSBTAG00000005796	1 retrocopy	retro_btau_1853,
Canis familiaris	ENSCAFG00000031010	1 retrocopy	retro_cfam_223,
Callithrix jacchus	ENSCJAG00000005913	1 retrocopy	retro_cjac_1322,
Echinops telfairi	ENSETEG00000012876	1 retrocopy	retro_etel_654,
Felis catus	ENSFCAG00000003925	1 retrocopy	retro_fcat_14,
Mustela putorius furo	ENSMPUG00000013949	1 retrocopy	retro_mputfur_173,
Mus musculus	ENSMUSG00000026554	1 retrocopy	retro_mmus_111,
Otolemur garnettii	ENSOGAG00000011349	1 retrocopy	retro_ogar_2113,
Pteropus vampyrus	ENSPVAG00000007982	1 retrocopy	retro_pvam_1356,
Sus scrofa	ENSSSCG00000006388	1 retrocopy	retro_sscr_88,
Tupaia belangeri	ENSTBEG00000001566	1 retrocopy	retro_tbel_3644,