RetrogeneDB ID: retro_opri_1025

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_59080:3655..4238(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BRMS1L
• Ensembl ID: ENSOPRG00000017354
• Aliases: None
• Description: breast cancer metastasis-suppressor 1-like [Source:HGNC Symbol;Acc:20512]

Sequence

>retro_opri_1025
ATGCCGGTGCATTCCCCCGGGGGGGATAAGAAGGAGACAAACGATCACCAATGAGATGGAGGTGAACCACTCTGAGAATG
AAGGGAGTAGCTCCGAGGACTAGGACACCGAGAGCTCGTCAGTCTCGGAGGATGGCGACAGCTCAGAAATAGATGATGAA
GACTGTGAAAGAAGAAGAATGGAATGTTCAGATGAAATGTCCAATCTTGAAAAACAGTTTACCGACCTCAGAGATCAATT
TTATAAAGAGCGATTAAGTCAGGTGAATGCAAAACTACAAGATGGCATAGATGGGAAAGCACCAGAATATTTGGAACCAC
TGGCAACTCTACAAGAAAATATGCAAATTCATACAAAGGTAGCAGGAATCTATAGGGAGCTCTGCTTAGTTTGTTCAGTA
AAGAACAAATATGAATGTGAAATTCAAGCTTCTTGCCAGCATTGTGAGAGTGAGAAGTTTTTGTTATAGGATACAGTCCA
GAGTGAGCTGAAGAAGATACGAAGGCTTGAAGAGGACAGGCACAGCATCGACATTACCTCAGAGCTGTGGAATGATGAGC
TGCAGTCAAGAAAGAAGAGGAGG

Alignment

ORF - retro_opri_1025 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 59.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPVHSRG-DKKETNHH-DEMEVDYAENEGSSSEDEDTESSSVSEDGDSSEMDDEDCERRRMECLDEMSNL
          MPVHS.G.DKKETN.H..EMEV...ENEGSSSED.DTESSSVSEDGDSSE.DDEDCERRRMEC.DEMSNL
Retrocopy MPVHSPGGDKKETNDH>NEMEVNHSENEGSSSED*DTESSSVSEDGDSSEIDDEDCERRRMECSDEMSNL

Parental  EKQFTDLKDQLYKERLSQVDAKLQEVIAGKAPEYLEPLATLQENMQIRTKVA-IYRELCLV-SVKNKYKC
          EKQFTDL.DQ.YKERLSQV.AKLQ..I.GKAPEYLEPLATLQENMQI.TKVA.IYRELCLV.SVKNKY.C
Retrocopy EKQFTDLRDQFYKERLSQVNAKLQDGIDGKAPEYLEPLATLQENMQIHTKVAGIYRELCLVCSVKNKYEC

Parental  EIQAPRQHCESEKLLLYDTVQSELEEKIRRLEEDRHSIDITSELWNDELQSRKKRK
          EIQA..QHCESEK.LL.DTVQSEL..KIRRLEEDRHSIDITSELWNDELQSRKKR.
Retrocopy EIQASCQHCESEKFLL*DTVQSEL-KKIRRLEEDRHSIDITSELWNDELQSRKKRR

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_1025 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000016974	1 retrocopy	retro_ogar_2341,
Oreochromis niloticus	ENSONIG00000019497	1 retrocopy	retro_onil_62,
Ochotona princeps	ENSOPRG00000017354	1 retrocopy	retro_opri_1025 ,