RetrogeneDB ID: retro_amel_1294

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193161.1:692252..692711(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSRP1
• Ensembl ID: ENSAMEG00000012114
• Aliases: None
• Description: cysteine and glycine-rich protein 1 [Source:HGNC Symbol;Acc:2469]

Sequence

>retro_amel_1294
GGAGCCGGAAACAATTGTGGGGTCTGTGGAGCGCTGTGAACCTTGTGGAGAAGGTCCAGGGTCCTGGAAGAAGTGTTCAC
CGACTGCTGCTTTCTGTGCATGGATTGCAGGACAAATTTAGACGGCATAGTGGTAGTGATGCATGATGAAGAGATCTACT
TGCAAATCTTACTATGGAAAGAAGGATGGGCTGAAAGGCTACTGTTGCAGCCAGGGCACTGGCGCACTCAACATGGACGG
TGAGGAGAGGCTGGGCATCAAACCCAAGTTCAACCTCACATGATTATGACAAATCCAAACACTTCTTAATTTGCTCAGAA
ATGCAGAGGTACGGAGAAGTATCCCACATATGGGGATTCTGTATATGCTGCTGAGAAGATAATTGGAGCTGGATAACCCT
AGCACAAAAACTGTTTCCTAAGTGCCAAGTGTGGGAAGGATCTTGAACCAACAACTCTA

Alignment

ORF - retro_amel_1294 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.8 %
• Parental protein coverage: 79.79 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GGGKKCGVCQ-KTVYFAEEVQCEGSSFHK-SCFLCMVCKKNLDSTTVAVHGEEIY-CKSCYGKKYGPKGY
          G.G..CGVC....V...E.VQ..G.S.H...CFLCM.C..NLD...V..H.EEIY.CKS.YGKK.G.KGY
Retrocopy GAGNNCGVCG<SAVNLVEKVQGPGRSVHR>CCFLCMDCRTNLDGIVVVMHDEEIY>CKSYYGKKDGLKGY

Parental  GYGQGAGTLSTDKGESL-GIRHEEAPGHRPTTNPNASKFAQKIGGSERCPRCSQAVYAAEKVIGAGKSWH
          ...QG.G.L..D..E.L.G......P.H...TNPN.S.FAQK..G.E..P.....VYAAEK.IGAG...H
Retrocopy CCSQGTGALNMDGEERL<GHQTQVQP-HMIMTNPNTS*FAQKCRGTEKYPTYGDSVYAAEKIIGAG*P*H

Parental  KSCFRCAKCGKGLESTTL
          K.CF..AKCGK.LE.TTL
Retrocopy KNCFLSAKCGKDLEPTTL

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_1294 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1294 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012114	1 retrocopy	retro_amel_1294 ,
Echinops telfairi	ENSETEG00000017067	1 retrocopy	retro_etel_417,
Macaca mulatta	ENSMMUG00000020772	1 retrocopy	retro_mmul_1505,
Mus musculus	ENSMUSG00000026421	1 retrocopy	retro_mmus_2226,
Pan troglodytes	ENSPTRG00000001836	2 retrocopies	retro_ptro_1920, retro_ptro_1922,
Tupaia belangeri	ENSTBEG00000008991	1 retrocopy	retro_tbel_2176,
Drosophila melanogaster	FBgn0259209	1 retrocopy	retro_dmel_71,