RetrogeneDB ID: retro_amel_5

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192344.1:3482706..3483612(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000020132
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000011723
• Aliases: None
• Description: None

Sequence

>retro_amel_5
ATGAAGTCCAATCCTGCCATCCAAGCCGCCATCGACCTGACAGCGGGCGCGGTGGGGGGCACGGCTTGTGTCCTGACCGG
GCAGCCTTTCGACACAGTGAAAGTGAAGATGCAGACGTTCCCCGGCCTGTACAAGGGCCTCACCGACTGCTGCCTGAAAA
CGTACTCCCAAGTGGGCCTGCGGGGCTTCTACAAAGGAACCGGCCCTGCGCTGATGGCCTACGTCGCCGAGAACTCTGTC
CTCTTCATGTGCTATGGCTTCTGCCAAGAGCTGGTGAGGAAGGTGGTTGGACTGGACAAGCAGGCGAAGCTGAGTGATCT
GCAGACGGCCACTGCGGGTTCCTTCGCCTCGGCGTTTGCTGCGCTGGCCCTGTGCCCCACTGAGCTTGTGAAGTGCCGGC
TACAGACCATGTACGAAATGGAGATGTCAGGGAAAATAGCAAAAAGCCAAGATACAATCTGGTCCGTCGTGAAGAGTATC
CTTAGAAAGGAAGGCCCCTTGGGCTTCTACCAAGGACTCTCGAGCACCCTCCTTCAAGAGGTACCAGGCTATTTCTTCTT
CTTCGGTGGCTATGAACTGAGTAGATCATTTTTTGCCTCAGGGAGATCAAAAGATGAACTAGGCCCTGTCCCTTTGATGT
TAAGTGGTGGAATTGCTGGAATTTGTCTTTGGCTTGTCATATACCCGGTGGATTGTATCAAATCCAGAATTCAGGTTCTT
TCCATGTCTGGGAAACAGGCTGGGTTTCTGGCAACTCTTACAAGTATTGTGAAAAATGAAGGAATAGCAGCCTTATATTC
TGGACTGACAGCTACTATGATTCGAGCAGTCCCTGCCAATGGGTCACTGTTTTTGGCTTATGAATATAGCAGGAGAATGA
TGATGAGCCAGTTTGAAGCATACTGA

Alignment

ORF - retro_amel_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.05 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKSSPAIQAAIDLTAGAAGGTACVLTGQPFDTLKVKMQTFPSLYRGLTDCCLKTYSQVGFRGFYKGTSPA
          MKS.PAIQAAIDLTAGA.GGTACVLTGQPFDT.KVKMQTFP.LY.GLTDCCLKTYSQVG.RGFYKGT.PA
Retrocopy MKSNPAIQAAIDLTAGAVGGTACVLTGQPFDTVKVKMQTFPGLYKGLTDCCLKTYSQVGLRGFYKGTGPA

Parental  LIANIAENSVLFMCYGFCQQVVRKVAGLEKQARLSDLQNAAAGSFASAFAALVLCPTELVKCRLQTMYEM
          L.A..AENSVLFMCYGFCQ..VRKV.GL.KQA.LSDLQ.A.AGSFASAFAAL.LCPTELVKCRLQTMYEM
Retrocopy LMAYVAENSVLFMCYGFCQELVRKVVGLDKQAKLSDLQTATAGSFASAFAALALCPTELVKCRLQTMYEM

Parental  ESSGKIARSQNTVWSMVKTVLRKDGPLGFYHGLSSTLLREVPGYFFFFGGYELSRSFFASGRSKDELGPV
          E.SGKIA.SQ.T.WS.VK..LRK.GPLGFY.GLSSTLL.EVPGYFFFFGGYELSRSFFASGRSKDELGPV
Retrocopy EMSGKIAKSQDTIWSVVKSILRKEGPLGFYQGLSSTLLQEVPGYFFFFGGYELSRSFFASGRSKDELGPV

Parental  PLMLSGGVGGICLWLAVYPVDCVKSRIQVLSMSGKQAGFIGTVISIVRNEGITALYSGLKPTMIRAFPAN
          PLMLSGG..GICLWL..YPVDC.KSRIQVLSMSGKQAGF..T..SIV.NEGI.ALYSGL..TMIRA.PAN
Retrocopy PLMLSGGIAGICLWLVIYPVDCIKSRIQVLSMSGKQAGFLATLTSIVKNEGIAALYSGLTATMIRAVPAN

Parental  GALFLAYEYSRKLMMSQFEAY
          G.LFLAYEYSR..MMSQFEAY
Retrocopy GSLFLAYEYSRRMMMSQFEAY

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_5 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_5 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011723	1 retrocopy	retro_amel_5 ,
Bos taurus	ENSBTAG00000011647	1 retrocopy	retro_btau_1581,
Canis familiaris	ENSCAFG00000005955	1 retrocopy	retro_cfam_211,
Choloepus hoffmanni	ENSCHOG00000004899	3 retrocopies	retro_chof_1643, retro_chof_494, retro_chof_561,
Erinaceus europaeus	ENSEEUG00000014870	1 retrocopy	retro_eeur_329,
Mus musculus	ENSMUSG00000031482	1 retrocopy	retro_mmus_75,
Oryctolagus cuniculus	ENSOCUG00000016684	2 retrocopies	retro_ocun_192, retro_ocun_1927,
Ochotona princeps	ENSOPRG00000014616	1 retrocopy	retro_opri_7,
Rattus norvegicus	ENSRNOG00000011881	1 retrocopy	retro_rnor_130,
Sorex araneus	ENSSARG00000002472	1 retrocopy	retro_sara_30,
Sus scrofa	ENSSSCG00000009373	1 retrocopy	retro_sscr_688,