RetrogeneDB ID: retro_opri_554

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_169974:8..713(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF138
• Ensembl ID: ENSOPRG00000011494
• Aliases: None
• Description: ring finger protein 138, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:17765]

Sequence

>retro_opri_554
GAAGATGATTTCTACTTGTCCCGTTCTGTCAGGAGGTGCTCAAAACGCCCGGTACGGACCTCGGCCTGTCAGCACGTTTT
CTGTAGAAAATGTTTCCTGACTGCAATGAGAGAAAAGTGGAATACATTGTCCCCTGTGTCGTGGAAAATGTGACTAGAAA
AGAAAGAGCATGTCCCGAACGGGCCCTTAGACCTTGAAAATATCATGAGGAAGTTTTCTGGTAGCTGCAGATGCTGTGCA
AAACAGATTAAATTCTATCGCATGAGACATCATTACAAATCTTGCAAGAAGTATCAAGATGAATATGGTGTGTCTTCTGT
CATTCCAAACTTACAGATTTCCCAAGATTCAGGAGGGAACAGTAATAGGAGTGAAACATCTACGTCAGATACCATAGAAA
CTTACCAAGAGAATACCAGTTCTTCTGGACATCCCACCTTTAAGTGTCCCTTGTGTCAAGAATCAAATCTTACCAGACAG
CGTTTATTGGATCACTGTAACAGTAATCACCTATTTCAGATAGTTCCTGTGACATGTCCTATTTGCGTGTCTCTTCCTTG
GGGAGATCCTACCCAGATTACTAGAAATTTCGTCAGTCATCTAAATCAAAGGCATCAGTTTGATTATGGAGAATTTGTGA
ATCTTCAGCTAGATGAGGAGACTCAGTACCAAACTGCTGTTGAAGAATCTTTTCAAGTAAATATC

Alignment

ORF - retro_opri_554 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.49 %
• Parental protein coverage: 95.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  EDDFY-CPV-CQEVLKTP-VRTSACQHVFCRKCFLTAMRE-SGIHCPLCRG-NVTRKERACPERA-LDLE
          EDDFY.CPV.CQEVLKTP.VRTSACQHVFCRKCFLTAMRE.SGIHCPLCRG.NVTRKERACPERA.LDLE
Retrocopy EDDFY>CPV>CQEVLKTP>VRTSACQHVFCRKCFLTAMRE>SGIHCPLCRG>NVTRKERACPERA>LDLE

Parental  NIMRKFSGSCRCCAKQIKFYRMRHHYKSCKKYQDEYGVSSVIPNLQISQDSGGNSNRSETSTSDTIETYQ
          NIMRKFSGSCRCCAKQIKFYRMRHHYKSCKKYQDEYGVSSVIPNLQISQDSGGNSNRSETSTSDTIETYQ
Retrocopy NIMRKFSGSCRCCAKQIKFYRMRHHYKSCKKYQDEYGVSSVIPNLQISQDSGGNSNRSETSTSDTIETYQ

Parental  ENTSSSGHPTFKCPLCQESNLTRQRLLDHCNSNHLFQIVPVTCPICVSLPWGDPTQITRNFVSHLNQRHQ
          ENTSSSGHPTFKCPLCQESNLTRQRLLDHCNSNHLFQIVPVTCPICVSLPWGDPTQITRNFVSHLNQRHQ
Retrocopy ENTSSSGHPTFKCPLCQESNLTRQRLLDHCNSNHLFQIVPVTCPICVSLPWGDPTQITRNFVSHLNQRHQ

Parental  FDYGEFVNLQLDEETQYQTAVEESFQVNI
          FDYGEFVNLQLDEETQYQTAVEESFQVNI
Retrocopy FDYGEFVNLQLDEETQYQTAVEESFQVNI

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_554 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 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000009856	1 retrocopy	retro_eeur_430,
Monodelphis domestica	ENSMODG00000010850	4 retrocopies	retro_mdom_1468, retro_mdom_387, retro_mdom_708, retro_mdom_725,
Mus musculus	ENSMUSG00000024317	2 retrocopies	retro_mmus_3726, retro_mmus_494,
Ochotona princeps	ENSOPRG00000004732	2 retrocopies	retro_opri_368, retro_opri_709,
Ochotona princeps	ENSOPRG00000011494	1 retrocopy	retro_opri_554 ,