RetrogeneDB ID: retro_amel_305

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192379.1:3127348..3127636(+)
• Located in intron of: ENSAMEG00000004889

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000007366
• Aliases: None
• Description: None

Sequence

>retro_amel_305
GGGAGGCCCCGTGGCTTCTGCAGTCGTCAAGGCCTAGGAGTTCACGGCAGCAAGACCAAGGAGGTGGAGTGGATGCCTGT
CACCAGCCTGTGCCGTCTGGTCAAGGACATAAAGTTCGGGTCCCTGGAGGAGACCTACCTCTTCCACCTGCCCATCAAGG
AATCTGAGATCATCGAGGTTTTCCTCGGATCGTCCTTCAAGGATGAGGTTTTGAAGATCATGCCCATGCAAAAGCAGACC
CATGCCGACAGGCAGACCGGGTTCAAGACATTTGTTGCCATAGGGGAT

Alignment

ORF - retro_amel_305 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.62 %
• Parental protein coverage: 72.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GRGRGRGRGRGRGARGGKAEDKEWIPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEV
          GR.RG.....G.G..G.K....EW.PVT.L.RLVKD.K..SLEE.YLF.LPIKESEII..FLG.S.KDEV
Retrocopy GRPRGFCSRQGLGVHGSKTKEVEWMPVTSLCRLVKDIKFGSLEETYLFHLPIKESEIIEVFLGSSFKDEV

Parental  LKIMPVQKQTRAGQRTRFKAFVAIGD
          LKIMP.QKQT.A...T.FK.FVAIGD
Retrocopy LKIMPMQKQTHADRQTGFKTFVAIGD

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_305 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_305 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 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002549	1 retrocopy	retro_acar_57,
Ailuropoda melanoleuca	ENSAMEG00000007366	1 retrocopy	retro_amel_305 ,
Cavia porcellus	ENSCPOG00000011651	11 retrocopies	retro_cpor_1030, retro_cpor_1238, retro_cpor_1376, retro_cpor_1469, retro_cpor_1527, retro_cpor_177, retro_cpor_19, retro_cpor_437, retro_cpor_718, retro_cpor_769, retro_cpor_808,
Macropus eugenii	ENSMEUG00000004508	2 retrocopies	retro_meug_156, retro_meug_2103,
Monodelphis domestica	ENSMODG00000016077	1 retrocopy	retro_mdom_536,
Sarcophilus harrisii	ENSSHAG00000015213	5 retrocopies	retro_shar_186, retro_shar_288, retro_shar_456, retro_shar_525, retro_shar_783,