RetrogeneDB ID: retro_amel_476

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192465.1:2147136..2147690(-)
• Located in intron of: ENSAMEG00000014673

Retrocopy information

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

Parental gene information

• Parental gene symbol: ITPA
• Ensembl ID: ENSAMEG00000011021
• Aliases: None
• Description: inosine triphosphatase (nucleoside triphosphate pyrophosphatase) [Source:HGNC Symbol;Acc:6176]

Sequence

>retro_amel_476
CTGAAGGAGGTCATTCAGATTCTAGGAAATAAGTTTCCATGAACTTTGGCGGCACAGAAAATTGACCTGCCAGAGTTCCA
GGGACAGCCCAATGAGATTTCCATACACAAGTGTCAGGAAACAGTTCACCAGGTACAGGGGCCTGTACTGGTGGAGGACA
CCCATCCATGCTTCAGTGCCTTTGGGAGCCTCTCTGGCCCCTACATAAAGTGGTTTCTGGAGAAGTTAAAGCCTGAAGGT
CTCTACCAGCTCCTGGCTGGGTTTGAGGACAGATTTGCCTGTGTGCTCTGCACATTTGTGCTCAGCATCAGGGACCCCAG
CAAGCCAGTGCCCCTGTTCAGGGGCCAGATCGTGGTACCCCAAGTCTTCCAGGACTTTGGCTGGGACCCCTGCTTTCAGC
CTGATGGATACGAGCAGGCACACGCAAAGATGCCCATAGCTGAGAAGAACACCATCTCCCATCACTTTCAGGCCCAGCTT
GAGCTACAAAAACACTTCTGCACCTGACTCTTCTGGTAGCCAGTGATGATTGCCCTGGCTGGGGATCTGGGGAA

Alignment

ORF - retro_amel_476 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.16 %
• Parental protein coverage: 90.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LEEVIQILGDKFPCTLVAQKIDQVPEYQGEPDEISIQKCQEAARQVQGPVLVEDTCLCFNALGGLPGPYI
          L.EVIQILG.KFP.TL.AQKID..PE.QG.P.EISI.KCQE...QVQGPVLVEDT..CF.A.G.L.GPYI
Retrocopy LKEVIQILGNKFP*TLAAQKID-LPEFQGQPNEISIHKCQETVHQVQGPVLVEDTHPCFSAFGSLSGPYI

Parental  KWFLEKLKPEGLYQLLAGFEDKSAYALCTFALSTGDPTEPVRLFRGRTSGRIVVPRGCRDFGWDPCFQPD
          KWFLEKLKPEGLYQLLAGFED..A..LCTF.LS..DP..PV.LFRG.....IVVP....DFGWDPCFQPD
Retrocopy KWFLEKLKPEGLYQLLAGFEDRFACVLCTFVLSIRDPSKPVPLFRG----QIVVPQVFQDFGWDPCFQPD

Parental  GYEQTYAEMPKAEKNAISHRFRALLELQKYFGS-LAPLTAGDDRPGRGAGE
          GYEQ..A.MP.AEKN.ISH.F.A.LELQK.F...L..L.A.DD.PG.G.GE
Retrocopy GYEQAHAKMPIAEKNTISHHFQAQLELQKHFCT<LTLLVASDDCPGWGSGE

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_476 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_476 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011021	1 retrocopy	retro_amel_476 ,
Canis familiaris	ENSCAFG00000031613	1 retrocopy	retro_cfam_1841,
Felis catus	ENSFCAG00000013414	1 retrocopy	retro_fcat_1776,
Microcebus murinus	ENSMICG00000013833	1 retrocopy	retro_mmur_1207,
Mustela putorius furo	ENSMPUG00000008868	1 retrocopy	retro_mputfur_971,
Mus musculus	ENSMUSG00000074797	3 retrocopies	retro_mmus_2063, retro_mmus_3369, retro_mmus_3604,