RetrogeneDB ID: retro_amel_1747

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194173.1:205334..205718(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BLOC1S5
• Ensembl ID: ENSAMEG00000017324
• Aliases: None
• Description: biogenesis of lysosomal organelles complex-1, subunit 5, muted [Source:HGNC Symbol;Acc:18561]

Sequence

>retro_amel_1747
ATGAGTGGTGGAGGGACGGAGACCCCTGTGGGTTGTGAGGCCACCCCGGGCGGCGGCGACAAGAAGAAGGATTCGCTGGG
GACTGCGGGCTCACCAGCACATTTCATTATCAAGGACCTTGGAGAAATTCATTCAAGGCTTTTAGATCACAGACCAGTTG
TTCAAGGAGAAACCCGTTATTTTGTGAAAGAATTTGAAGAAAAGCGTGGTCTTCGAGAAATGCAAGTTCTTGAAAATTTG
AAGAATATGATCCACGAAACAAATGAACATACTCTTCCCAAATGTAAAGAAATCATGCAAGACAACTTAAACCAAGTTCT
CCAGAGATTGCAAGCAGCTTCTGACTCAGTCTGCAGACTCCAGCAGAGGAAAGAAGGAACAAAA

Alignment

ORF - retro_amel_1747 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.53 %
• Parental protein coverage: 68.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGGGTETPVGCEATPGGGDKKKDSLGTAGSPAHFIIKDLGEIHSRLLDHRPVVQGETRYFVKEFEEKRG
          MSGGGTETPVGCEATPGGGDKKKDSLGTAGSPAHFIIKDLGEIHSRLLDHRPVVQGETRYFVKEFEEKRG
Retrocopy MSGGGTETPVGCEATPGGGDKKKDSLGTAGSPAHFIIKDLGEIHSRLLDHRPVVQGETRYFVKEFEEKRG

Parental  LREMRVLENLKNMIHETNEHTLPKCREIMQDNLNQVLQRLQAASDSICRLQQREQEQK
          LREM.VLENLKNMIHETNEHTLPKC.EIMQDNLNQVLQRLQAASDS.CRLQQR....K
Retrocopy LREMQVLENLKNMIHETNEHTLPKCKEIMQDNLNQVLQRLQAASDSVCRLQQRKEGTK

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_1747 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1747 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 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017324	1 retrocopy	retro_amel_1747 ,
Bos taurus	ENSBTAG00000039732	2 retrocopies	retro_btau_1699, retro_btau_1747,
Monodelphis domestica	ENSMODG00000010026	1 retrocopy	retro_mdom_1483,
Oryctolagus cuniculus	ENSOCUG00000025755	2 retrocopies	retro_ocun_1051, retro_ocun_269,
Otolemur garnettii	ENSOGAG00000030827	1 retrocopy	retro_ogar_2470,
Ictidomys tridecemlineatus	ENSSTOG00000027342	3 retrocopies	retro_itri_1038, retro_itri_179, retro_itri_1901,