RetrogeneDB ID: retro_amel_1075

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192883.1:456760..457076(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAR1B
• Ensembl ID: ENSAMEG00000017849
• Aliases: None
• Description: SAR1 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:10535]

Sequence

>retro_amel_1075
ATGTTCTTCATATTTGAGTGAATTTATAGTGGGTTCAGCAGTATGCTACAGTTTTTAGAATTATATAAGAAAACTGGCGA
ATTGCTATTTTTTGGATTGTTCAATGTGAGAAAACAACATTGCCACTTATGCTAAAAGATGGCAGATTTGCACAACATGT
CACAGGTTAGCTCCCACTTCAGAAGAACCAGCCATTGCTGGCATGACCATTATACCTTTCGATCTGGGTGGACATGTCAA
GCTGGAAGAGTGTGGAAATACGACCTTCCTGCCACCAAGTGCTGTTGTACTTCTGGTGGACAGTGCAGACCATGAA

Alignment

ORF - retro_amel_1075 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.36 %
• Parental protein coverage: 53.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSFIFDWIYSGFSSVLQFLGLYKKTGKLVFLGLDN-AGKTTLLHMLKDDRLGQHVP-TLHPTSEELTIAG
          M.FIF..IYSGFSS.LQFL.LYKKTG.L.F.GL.N...KTTL..MLKD.R..QHV...L.PTSEE..IAG
Retrocopy MFFIFE*IYSGFSSMLQFLELYKKTGELLFFGLFN<CEKTTLPLMLKDGRFAQHVT<RLAPTSEEPAIAG

Parental  MTFTTFDLGGHV-QARRVWKNYLPAI-NGIVFLVDCADHE
          MT...FDLGGHV.QA.RVWK..LPA.....V.LVD.ADHE
Retrocopy MTIIPFDLGGHV<QAGRVWKYDLPAT>SAVVLLVDSADHE

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_1075 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1075 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017849	1 retrocopy	retro_amel_1075 ,
Ailuropoda melanoleuca	ENSAMEG00000017868	1 retrocopy	retro_amel_1698,
Dasypus novemcinctus	ENSDNOG00000013784	3 retrocopies	retro_dnov_1584, retro_dnov_1804, retro_dnov_919,
Loxodonta africana	ENSLAFG00000001021	1 retrocopy	retro_lafr_1043,
Oryctolagus cuniculus	ENSOCUG00000008250	1 retrocopy	retro_ocun_1004,
Pteropus vampyrus	ENSPVAG00000012433	2 retrocopies	retro_pvam_1219, retro_pvam_725,
Tursiops truncatus	ENSTTRG00000016864	2 retrocopies	retro_ttru_1225, retro_ttru_857,