RetrogeneDB ID: retro_opri_792

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_31089:4713..5175(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTAP
• Ensembl ID: ENSOPRG00000001259
• Aliases: None
• Description: methylthioadenosine phosphorylase [Source:HGNC Symbol;Acc:7413]

Sequence

>retro_opri_792
CTTGGTGATACGGGCCTGGATGATCCATGAATTTTAGAAGGAAGAAGTGAAAAATATGTGTATACTCCATCTGGCAAGCC
ATTGCATGCCTCGATTTTGGGGAAAATAAAAAATGTTGATTGTGTATTCCTTACAAGGCACGGGAGGCAGCACACCATCA
TGCCTTCCAAAGTGAACTACCAGGCGAACTTCGGGGCCTTGAAGGAGGAAGACTATGTACGTCATAGTGATCACAGCTTG
TGGCTTCCTGAGGAAGAGAATCAGCCCCGTGATATTGTCATTACCAGTCAGTTCATCCACAGCACAACCCACAAGGCCTC
AGTTTTCTGATGGAAGCCATTCCTGTGCTCAAGAAATGTGCCATATTTTAATAGCCAAGCCATTTTTCCCAAAACAAGAG
AAGTTCTCATAGAGAATGCTAAGAAGCTAGGACTCCAGTGCCACTCAAAGGAGACCAGGCTT

Alignment

ORF - retro_opri_792 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.25 %
• Parental protein coverage: 55.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IGGTGLDDPEILEGRTEKYVDTPFGKXXXXXXXXXXXXXXXXXXXXHGRQHTIMPSKVNYQANIWALKEE
          .G.TGLDDP.ILEGR.EKYV.TP.GK....................HGRQHTIMPSKVNYQAN..ALKEE
Retrocopy LGDTGLDDP*ILEGRSEKYVYTPSGKPLHASILGKIKNVDCVFLTRHGRQHTIMPSKVNYQANFGALKEE

Parental  GCTH-VLVTTACGSLR-EEIQPGDIVIIDQFIDRTT-TRPQTFYDGSHSCARGVCHIPMVEPF-CPKTRE
          ........T.ACG.LR.EE.QP.DIVI..QFI..TT.TRPQ.F.DGSHSCA...CHI....PF..PKTRE
Retrocopy DYVR>IVIT-ACGFLR<EENQPRDIVITSQFIHSTT>TRPQ-FSDGSHSCAQEMCHILIAKPF<FPKTRE

Parental  VLIETAKKLGLRCHSKGTMI
          VLIE.AKKLGL.CHSK.T..
Retrocopy VLIENAKKLGLQCHSKETRL

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_792 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002224	1 retrocopy	retro_chof_772,
Callithrix jacchus	ENSCJAG00000008021	2 retrocopies	retro_cjac_187, retro_cjac_950,
Cavia porcellus	ENSCPOG00000000825	1 retrocopy	retro_cpor_375,
Dasypus novemcinctus	ENSDNOG00000008670	1 retrocopy	retro_dnov_1572,
Echinops telfairi	ENSETEG00000013214	1 retrocopy	retro_etel_588,
Macropus eugenii	ENSMEUG00000015381	2 retrocopies	retro_meug_807, retro_meug_917,
Microcebus murinus	ENSMICG00000015072	1 retrocopy	retro_mmur_927,
Macaca mulatta	ENSMMUG00000001137	1 retrocopy	retro_mmul_1549,
Ornithorhynchus anatinus	ENSOANG00000013963	1 retrocopy	retro_oana_38,
Oryctolagus cuniculus	ENSOCUG00000012289	2 retrocopies	retro_ocun_1355, retro_ocun_341,
Otolemur garnettii	ENSOGAG00000007889	1 retrocopy	retro_ogar_3285,
Ochotona princeps	ENSOPRG00000001259	1 retrocopy	retro_opri_792 ,