RetrogeneDB ID: retro_amel_1292

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193157.1:769466..770060(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRR1
• Ensembl ID: ENSAMEG00000006437
• Aliases: None
• Description: KRR1, small subunit (SSU) processome component, homolog (yeast) [Source:HGNC Symbol;Acc:5176]

Sequence

>retro_amel_1292
CTCATTGGTCCCAAAGGATCTACACTGAAGGCTTTGGAACTCTTAACAAACTGTTATGTTATGGTTCAGGGAAAAATGGT
TTCAGTGATTGGACCTTTTAGTGGCTTAAAAGAGGTTCGAAAAGTAGTCTGAGATACTATGAAGAATATTCGTCCAGTTT
ATAACATTAAAACCTTAATGATTAAATGAGAGTGGGCAAAAGATTCTGAATTAAAATCACAAAGTTGGGAAAGATTTTTG
CCACAGTTCAAGCACAAGAATGTGAATAAATGCAAGGAACCAAAGAAAAAAACTGTCAAGAAAGAGTACACACCATTCCC
ACTATCACAGTCGGAAAGATTGGTAAAGAATTAGCTAGTGGTGAATATTTTCTGAAGGCAAGTCAAAAGAAGTGACAGAA
AATGGAAGCAATAAAGGCTAAACAAGAGGAAGCTCTCGGGTAAGAGACAACAGGAAAGAAACAAAGCTTTTATTCCACCT
AAAGAAAAACCAGTTGTGAAACCAGAGGAAGCTTCTACTGAAAATAAAATTGATGTGGCTGCCATCAAGGAACAGGTTAA
GAAAGTAAAGAATAAGAAACTGGGAGGTCTTTCA

Alignment

ORF - retro_amel_1292 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.59 %
• Parental protein coverage: 52.37 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LIGPKGSTLKALELLTNCYIMVQGNTVSVIGPFSGLKEVRKVVLDTMKNIHPIYNIKTLMIKRELAKDSE
          LIGPKGSTLKALELLTNCY.MVQG..VSVIGPFSGLKEVRKVV.DTMKNI.P.YNIKTLMIK.E.AKDSE
Retrocopy LIGPKGSTLKALELLTNCYVMVQGKMVSVIGPFSGLKEVRKVV*DTMKNIRPVYNIKTLMIK*EWAKDSE

Parental  LRSQSWERFLPQFKHKNVNKCKEPKKKTVKK-EYTPFPPPQPESQIDKELASGEYFLKASQKKRQKMEAI
          L.SQSWERFLPQFKHKNVNKCKEP.KK...K.E.....P......I.KELASGEYFLKASQKK.QKMEAI
Retrocopy LKSQSWERFLPQFKHKNVNKCKEP-KKKTVK<ERVHTIPTITVGKIGKELASGEYFLKASQKK*QKMEAI

Parental  KAKQAEAL-SKRQEERNKAFIPPKEKPVVKPKEASTENKIDVAAIKEKVKKAKNKKLGALS
          KAKQ.EAL..KRQ.ERNKAFIPPKEKPVVKP.EASTENKIDVAAIKE.VKK.KNKKLG.LS
Retrocopy KAKQEEAL>GKRQQERNKAFIPPKEKPVVKPEEASTENKIDVAAIKEQVKKVKNKKLGGLS

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_1292 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1292 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 5 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006437	1 retrocopy	retro_amel_1292 ,
Canis familiaris	ENSCAFG00000005665	1 retrocopy	retro_cfam_1091,
Choloepus hoffmanni	ENSCHOG00000009636	5 retrocopies	retro_chof_1030, retro_chof_1826, retro_chof_2438, retro_chof_2452, retro_chof_365,
Monodelphis domestica	ENSMODG00000020451	1 retrocopy	retro_mdom_791,
Tupaia belangeri	ENSTBEG00000008145	5 retrocopies	retro_tbel_1056, retro_tbel_2060, retro_tbel_2911, retro_tbel_2915, retro_tbel_3679,