RetrogeneDB ID: retro_amel_590

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192513.1:1828739..1829098(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000009245
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: C1orf21
• Ensembl ID: ENSAMEG00000013468
• Aliases: None
• Description: chromosome 1 open reading frame 21 [Source:HGNC Symbol;Acc:15494]

Sequence

>retro_amel_590
ATGGGCTGTGCCTCTGCCAAGCATGTTGCCACTGTTCAAAAGAGGAAGCCCAGAAAGGGAAGAACTACCAGAACTGAGAT
GTGTTTGGCGACGAGTATAGGATCAAACCGGTGGAAGAGGTCAGGTACATGAAAAATGTGGCAGAGGAGGAGCAGAAAAT
AGCACCAGGAACCAAGAAAACTTGGAAAAAAGTGCCGTTTCTAACGTTAAGACTTAAAACTAATGAAGAGATTCCACTAT
TAGTTCATCAGCTGAGAGCAAATGTGAACATCTCTGAAAGCCAACAAGAATTCTTCAGAATGCTGGATGAAAAAATTGAA
AAACGTCGAGATTACTATTCCGGAGAAGAGGATATCACA

Alignment

ORF - retro_amel_590 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.68 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGCASAKHVAAVQ-SEEDAQKGKNYQNGDVFGDEYRIKPVEEVKYMKNGAEEEQKIA-ARNQENLEKSAS
          MGCASAKHVA.VQ..EE.AQKGKNYQN.DVFGDEYRIKPVEEV.YMKN.AEEEQKIA..RNQENLEKSA.
Retrocopy MGCASAKHVATVQ<KEE-AQKGKNYQN*DVFGDEYRIKPVEEVRYMKNVAEEEQKIA<TRNQENLEKSAV

Parental  SNV-RLKTNKEIPGLVHQPRANMHISESQQEFFRMLDEKIEKGRDYCSEEEDIT
          SNV.RLKTN.EIP.LVHQ.RAN..ISESQQEFFRMLDEKIEK.RDY.S.EEDIT
Retrocopy SNV>RLKTNEEIPLLVHQLRANVNISESQQEFFRMLDEKIEKRRDYYSGEEDIT

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_590 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_590 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013468	2 retrocopies	retro_amel_508, retro_amel_590 ,
Bos taurus	ENSBTAG00000038079	3 retrocopies	retro_btau_1219, retro_btau_1661, retro_btau_18,
Canis familiaris	ENSCAFG00000013460	1 retrocopy	retro_cfam_1069,
Mustela putorius furo	ENSMPUG00000011816	1 retrocopy	retro_mputfur_1583,
Sorex araneus	ENSSARG00000013999	1 retrocopy	retro_sara_185,