RetrogeneDB ID: retro_amel_675

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192563.1:1487009..1487866(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNN1
• Ensembl ID: ENSAMEG00000000062
• Aliases: None
• Description: calponin 1, basic, smooth muscle [Source:HGNC Symbol;Acc:2155]

Sequence

>retro_amel_675
ATGTCCTTTGCTCACTTCAACCAGGGCCCCACCTATGGGTTGTCTGTTGAGGTCGAGAACAAACTGGCCCAAAAGTACTA
TCACAAGCAGGAGTGGGAGCTTCGAGAATGGATCGAGGGGGTGATAGGGCACAGCATCGGCAACAATTTCATGGACGGCC
TCTAAGATGGCATCATTCTTTGCAAGTTCATCAGTAAGTTCCAGCCAGGCTCCATGAAAAAGGTCGGTAAGTCGACCCAA
AATTGGCACCTGCTGGAAAACATTGGCAACTGCATCAAGGCCATCACCAAATATAGGGTGAGGGCCCATGACATTTTTGA
GGCCCATGACCTGTTTGAGAATACCGACCGCACCCAGGTGCAGTGCACACCCCCAGCCGTGGCTAAGATGAAAGGGAATA
AAGTGAGTGTAGGGGTGAAGTATGCAGAGAAGCAGGAACAGAAATTTGAGCCAGAGAAGCTAAGAGAAGGGCAGAACATC
ATCAGGCTACAGATGGGCGCCAACAGGTTTGCTAGCCAGCAGGGCATGACGGCCTATGGCCCCCGGCGCCACCTCTATGA
CCCCAAGCTGGGTAAGGACCAGCGCCTGGTCTAGGCCACCATCAGCCTGCAGGTAGTTACCAACAAGGGAGCCAGCCAGG
CCAGCCTGACTGCACCTGGGACCAAGCAACAGATCGTCAAGCCAGGGCTGGGCATGGAGCACTGTGACGTGCTCAACGCC
AGTCTGCAGATGGGCAGCAACAAGGAGGCCTCATGGCAGAGCGTGACAGTGCCAGGTCTGTGACCCCAAGTACTACCTGA
TGCCTCAATACTCAGCCGGGCGAGCCTACCCACAACCACCGCCCACACAACTACTAC

Alignment

ORF - retro_amel_675 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.07 %
• Parental protein coverage: 97.31 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSAHFNRGPAYGLSAEVKNKLAQKYDHQREQELREWIEGVTGRRIGNNFMDGLKDGIILCEFINKLQPG
          MS.AHFN.GP.YGLS.EV.NKLAQKY.H..E.ELREWIEGV.G..IGNNFMDGL.DGIILC.FI.K.QPG
Retrocopy MSFAHFNQGPTYGLSVEVENKLAQKYYHKQEWELREWIEGVIGHSIGNNFMDGL*DGIILCKFISKFQPG

Parental  SVKKVNESTQNWHQLENIGNFIKAITKYGVKPHDIFEANDLFENTNHTQVQSTLLALASMAKTKGNKVNV
          S.KKV..STQNWH.LENIGN.IKAITKY.V..HDIFEA.DLFENT..TQVQ.T..A.A.M...KGNKV.V
Retrocopy SMKKVGKSTQNWHLLENIGNCIKAITKYRVRAHDIFEAHDLFENTDRTQVQCTPPAVAKM---KGNKVSV

Parental  GVKYAEKQERKFEPEKLREGRNIIGLQMGTNKFASQQGMTAYGTRRHLYDPKLGTDQPLDQATISLQMGT
          GVKYAEKQE.KFEPEKLREG.NII.LQMG.N.FASQQGMTAYG.RRHLYDPKLG.DQ.L..ATISLQ..T
Retrocopy GVKYAEKQEQKFEPEKLREGQNIIRLQMGANRFASQQGMTAYGPRRHLYDPKLGKDQRLV*ATISLQVVT

Parental  NKGASQAGMTAPGTKRQIFEPGLGMEHCDTLNVSLQMGSNKGASQRGMTVYGLPRQVYDPKYCLT-PDYP
          NKGASQA..TAPGTK.QI..PGLGMEHCD.LN.SLQMGSNK.AS....TV.GL..QV......L..P..P
Retrocopy NKGASQASLTAPGTKQQIVKPGLGMEHCDVLNASLQMGSNKEASWQSVTVPGL*PQVLPDASILS<PGEP

Parental  ELGEPAHNHH
          ......HN..
Retrocopy THNHRPHNYY

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_675 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_675 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000062	1 retrocopy	retro_amel_675 ,
Ailuropoda melanoleuca	ENSAMEG00000016707	1 retrocopy	retro_amel_1412,
Ailuropoda melanoleuca	ENSAMEG00000018148	1 retrocopy	retro_amel_1893,
Callithrix jacchus	ENSCJAG00000005530	1 retrocopy	retro_cjac_681,
Tursiops truncatus	ENSTTRG00000001803	1 retrocopy	retro_ttru_1792,