RetrogeneDB ID: retro_opri_443

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_122691:697..1114(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP1S3
• Ensembl ID: ENSOPRG00000013358
• Aliases: None
• Description: adaptor-related protein complex 1, sigma 3 subunit [Source:HGNC Symbol;Acc:18971]

Sequence

>retro_opri_443
ATGCAGTTTATGTTGGTTTTTAGTCGTCAGGGGAAGCTTCGACTGCAGAAATGGTATGTGCCACTGTCAGACAAAGAGAA
GAAAAAGATCACAAGAGAACTTGTTCAGACCGTCTTAGCACGGAAACCAAAAAGGTGCAACTTTCTCAAGTGGCGAGATC
TGAAGATTGTTTATAAAAGGTACGCAAGTCTGTATTTCTGCTGTGCCATTGAGGACCAGGACAATGAACTCATTACCCTG
GAAATAATTCATCGCTATGTGGAGTTACTCGACAAGTATTTTGGCAGCGTGTGTGAACTTGATATTATCTTCAATTTTGA
GGCGGCTTACTTTATTTTGGATGAGTTTCTTTTGGGAGGAGAAGTTCAAGAAACATCCAAGAAAAATGTCCTTAAACCCA
TTGAACAGGCTGATCTG

Alignment

ORF - retro_opri_443 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.66 %
• Parental protein coverage: 97.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IHFILLFSRQGKLRLQKWYTTLSDKERKKITREIVQIILSRGHRTSSFVDWKELKLVYKRYASLYFCCAV
          ..F.L.FSRQGKLRLQKWY..LSDKE.KKITRE.VQ..L.R......F..W..LK.VYKRYASLYFCCA.
Retrocopy MQFMLVFSRQGKLRLQKWYVPLSDKEKKKITRELVQTVLARKPKRCNFLKWRDLKIVYKRYASLYFCCAI

Parental  ENQDNELLTLEVVHRYVELLDKYFGNVCELDIIFNFEKAYFILDEFIIGGEVQETSKKVAVKAIEDSDM
          E.QDNEL.TLE..HRYVELLDKYFG.VCELDIIFNFE.AYFILDEF..GGEVQETSKK...K.IE..D.
Retrocopy EDQDNELITLEIIHRYVELLDKYFGSVCELDIIFNFEAAYFILDEFLLGGEVQETSKKNVLKPIEQADL

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_443 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 9 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011939	5 retrocopies	retro_chof_113, retro_chof_1230, retro_chof_1299, retro_chof_1949, retro_chof_2099,
Callithrix jacchus	ENSCJAG00000012352	2 retrocopies	retro_cjac_3187, retro_cjac_3903,
Macropus eugenii	ENSMEUG00000016580	11 retrocopies	retro_meug_1074, retro_meug_1342, retro_meug_1488, retro_meug_168, retro_meug_1864, retro_meug_289, retro_meug_318, retro_meug_361, retro_meug_816, retro_meug_909, retro_meug_938,
Microcebus murinus	ENSMICG00000014406	1 retrocopy	retro_mmur_1492,
Monodelphis domestica	ENSMODG00000021198	1 retrocopy	retro_mdom_1427,
Mus musculus	ENSMUSG00000054702	3 retrocopies	retro_mmus_2202, retro_mmus_2799, retro_mmus_487,
Ochotona princeps	ENSOPRG00000013358	1 retrocopy	retro_opri_443 ,
Pan troglodytes	ENSPTRG00000012979	1 retrocopy	retro_ptro_2258,
Sarcophilus harrisii	ENSSHAG00000010973	1 retrocopy	retro_shar_695,