RetrogeneDB ID: retro_opri_234

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_4011:51869..52346(-)
• Located in intron of: ENSOPRG00000001638

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUSD3
• Ensembl ID: ENSOPRG00000005344
• Aliases: None
• Description: sushi domain containing 3 [Source:HGNC Symbol;Acc:28391]

Sequence

>retro_opri_234
CAGGAGTCCCTGGGCTTCAAGGTGGCCGTGACTGCCTCCATCGTGAGCTGTGCTATCATCCTGCTCATGTCCGTGGCCTT
CCTCACCTGCTGTCTCCTTAAATGCATGAAGAGGAGTGAGCAGCGGCGTTCTAACAGGTCAACCCAGCTGTGGCACCAGC
TGAGAGGTGAGGACCTGGAGACAGTGCAGGCTGCGTATCTGGGCATCAAGGGCCTCAACTTCAACAACAGCAACAGCAGC
CCAAGGAACCAGCGTGCTCAAGCGCATGACAATCACGGCTTCACCAGAGAGCTCGAGGGCATCAGAGACCTGGACGGTGT
GACCCCCAGCGTGAACAAGGACCTCAGGAGCCTTGCACTTGGTGCTGTGAGTCTCAGCGGCCCCTCCAGCGGCTCCCACG
CCTGTGTGATGGTGCACACAGAACAACTGGGGCAGACCCTCTCTGCACCCGGGCCAAGCACAGCTCACTTTCCAGGA

Alignment

ORF - retro_opri_234 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.86 %
• Parental protein coverage: 82.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QESLGFKVAVIASIVSCAIILLMSVAFLTCCLLKCMKRSEQRRSNRSTQLWHQLRGEDLETVQAAYLGIK
          QESLGFKVAV.ASIVSCAIILLMSVAFLTCCLLKCMKRSEQRRSNRSTQLWHQLRGEDLETVQAAYLGIK
Retrocopy QESLGFKVAVTASIVSCAIILLMSVAFLTCCLLKCMKRSEQRRSNRSTQLWHQLRGEDLETVQAAYLGIK

Parental  GLNFNNSNSSPRNQRAQAHDNHSFTRELEGIRDLDGVTPSVDKDLRSLALGAVSPSGPSSSSHACVMVHT
          GLNFNNSNSSPRNQRAQAHDNH.FTRELEGIRDLDGVTPSV.KDLRSLALGAVS.SGPSS.SHACVMVHT
Retrocopy GLNFNNSNSSPRNQRAQAHDNHGFTRELEGIRDLDGVTPSVNKDLRSLALGAVSLSGPSSGSHACVMVHT

Parental  EQLGQTLSAPGPSTAHFPG
          EQLGQTLSAPGPSTAHFPG
Retrocopy EQLGQTLSAPGPSTAHFPG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_234 was not experimentally validated.

Homology

Retrocopy orthology:

Ochotona princeps 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001297	1 retrocopy	retro_acar_95,
Ochotona princeps	ENSOPRG00000005344	2 retrocopies	retro_opri_234 , retro_opri_581,
Rattus norvegicus	ENSRNOG00000016525	1 retrocopy	retro_rnor_1205,