RetrogeneDB ID: retro_opri_1119

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_73572:3783..4296(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000005929
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SRM
• Ensembl ID: ENSOPRG00000012079
• Aliases: None
• Description: spermidine synthase [Source:HGNC Symbol;Acc:11296]

Sequence

>retro_opri_1119
GATGTCATCCACCTCTCTAAGAAATTCCTGCCAGGGATGGCCGTTGGCTACTCCAGCCCAAAGCTAACCCTCTACATGGG
TGATGGCTTTGAGTTCATGAAGCAAAAGCAGGATGCCTTCGATGTCTTCATCACCGGCTCTTCCGATCCGATGCGCCCTG
CCGAGGGCCTCTTCAAAGAGTCCTACTACCAGCTCATGAAGACAGCGCTCAAGGAGGATGGTGTACTCTTGCCAGGGGGA
GTGCCAGTGGCTGCACTTGGACCTAATCAAGCAGATGTGGCAGTTCTGCAAGGCACCCTTCCCTGTGGGCTACGCCTACT
GTACCATCCCCACCTACCCTGGCGGGCAGATCATGCTGTGCAGCAAGAACCCGAACACCAACTTCCCGGAGCTAGCACAG
CAGCTAACACAGAAGCAGGTGGAGCAGATGCAGCTTAAGTACTACAACTCGGACGTGCATCGCGCTGCCTTCGTGCTGCC
CAAGTTTGCCCGCAGGCCCTGAATGACATCAGC

Alignment

ORF - retro_opri_1119 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.57 %
• Parental protein coverage: 57.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DVIHVSKKFLPGMAVGYSSPKLTLHVGDGFEFMKQNQDAFDVIITDSSDPMGPAESLFKESYYQLMKTAL
          DVIH.SKKFLPGMAVGYSSPKLTL..GDGFEFMKQ.QDAFDV.IT.SSDPM.PAE.LFKESYYQLMKTAL
Retrocopy DVIHLSKKFLPGMAVGYSSPKLTLYMGDGFEFMKQKQDAFDVFITGSSDPMRPAEGLFKESYYQLMKTAL

Parental  KEDGVL-CCQGECQWLHLDLIKQMRQFCKALFPVVGYAYCTIPTYPGGQIGFMLCSKNPSTNFAEPVQQL
          KEDGVL.C.QGECQWLHLDLIKQM.QFCKA.FP.VGYAYCTIPTYPGGQI..MLCSKNP.TNF.E..QQL
Retrocopy KEDGVL>C-QGECQWLHLDLIKQMWQFCKAPFP-VGYAYCTIPTYPGGQI--MLCSKNPNTNFPELAQQL

Parental  TQKQVEQMQLKYYNSDVHRAAFVLPEFARK-ALNDIS
          TQKQVEQMQLKYYNSDVHRAAFVLP.FAR..ALNDIS
Retrocopy TQKQVEQMQLKYYNSDVHRAAFVLPKFARR<ALNDIS

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_1119 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 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002354	4 retrocopies	retro_cjac_2131, retro_cjac_2524, retro_cjac_3331, retro_cjac_4025,
Gorilla gorilla	ENSGGOG00000014385	1 retrocopy	retro_ggor_1756,
Loxodonta africana	ENSLAFG00000028297	2 retrocopies	retro_lafr_1175, retro_lafr_894,
Macropus eugenii	ENSMEUG00000007002	2 retrocopies	retro_meug_1330, retro_meug_887,
Myotis lucifugus	ENSMLUG00000017585	1 retrocopy	retro_mluc_2458,
Macaca mulatta	ENSMMUG00000019321	2 retrocopies	retro_mmul_1500, retro_mmul_2259,
Ochotona princeps	ENSOPRG00000012079	1 retrocopy	retro_opri_1119 ,