RetrogeneDB ID: retro_opri_474

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_1328:48207..48848(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAPTM4A
• Ensembl ID: ENSOPRG00000012401
• Aliases: None
• Description: lysosomal protein transmembrane 4 alpha [Source:HGNC Symbol;Acc:6924]

Sequence

>retro_opri_474
ATGGTGTCTATGTCTTTGCAGAGCTGTGGCGACTGGTTCTACAGCACCCAGTGAGGCGCCTGTTGCTATGTCTGCACCGG
GACCATCATCCTGGGGATCTGTATATAGTGGCCAACCTATTGATGGCAATATTGCTGATTGTGGAAGTGACTCATCCAAA
CTTAATGCCCACTGTCAACAACATTCAGTATGAAGTCATTGGTAATTACTACTCGAGAAGCTGGCTGATAATGTTTGTGT
TCTTTTTGCCATCTCTGTTCTTACGTTTATAGTCAGTTCAGTGCTGCTATATGGGGCAATTTTTAATCAGGGAGGTTGGT
TGATCCCATTCTTCTGTTACGGGCTTTTGACTTCGTCCTCAGTTGTTCCCTCGCTATCAGTTCGCACTTGCCAAGGATCA
AAGAATATCTGGATCGGTTACCTGATTTTCCCTACAAAGACAACTCCTGGCCTTGGACTCCAGCTGCCTCTTGTTCATTT
TTCTCATGTTCTGTGTGCTCTTCATCGTCTTTAAGGCTTATCTAATCTACTGTGCGTGGAACTGCTACAAACATTTCAAC
AACAAAAACGAGCCAGAGATTGCTGTGTACCCTGTCTTTGAAGCACCTCCACAGTATGTGTTGCCGACCTATGAAATGGC
A

Alignment

ORF - retro_opri_474 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.58 %
• Parental protein coverage: 93.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MVSMTFKRSRGDRFYSVRCCGCCHVRTGTIILGTW-YMVVNLLMAILLIVEVTHPNLMPAVNNIQYEVIG
          MVSM....S.GD.FYS.....CC.V.TGTIILG...Y.V.NLLMAILLIVEVTHPNLMP.VNNIQYEVIG
Retrocopy MVSMSLQ-SCGDWFYSTQ*GACCYVCTGTIILGIC<YIVANLLMAILLIVEVTHPNLMPTVNNIQYEVIG

Parental  NYYSS-ERMADNVCVLFAVAVLTFIISSVLVYGAIFYQAGWLIPFFCY-RLFDFVLSCLVAISSLTYLPR
          N.Y.S.E..ADNVCVLFA..VLTFI.SSVL.YGAIF.Q.GWLIPFFCY.R.FDFVLSC..AISS...LPR
Retrocopy N-YYS<EKLADNVCVLFAISVLTFIVSSVLLYGAIFNQGGWLIPFFCY<RAFDFVLSCSLAISS--HLPR

Parental  IEEYLDQLPDFPYKDD-LLALDSSCLLFIVLMFCVVFIVFKAYLIYCVWNCYKYINSRNMPEIAVYPAFE
          I.EYLD.LPDFPYKD..LLALDSSCLLFI.LMFCV.FIVFKAYLIYC.WNCYK..N..N.PEIAVYP.FE
Retrocopy IKEYLDRLPDFPYKDN<LLALDSSCLLFIFLMFCVLFIVFKAYLIYCAWNCYKHFNNKNEPEIAVYPVFE

Parental  APPQYVLPTYEMA
          APPQYVLPTYEMA
Retrocopy APPQYVLPTYEMA

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_474 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020894	1 retrocopy	retro_btau_575,
Choloepus hoffmanni	ENSCHOG00000011200	2 retrocopies	retro_chof_1916, retro_chof_2320,
Callithrix jacchus	ENSCJAG00000007433	1 retrocopy	retro_cjac_839,
Echinops telfairi	ENSETEG00000002569	1 retrocopy	retro_etel_591,
Mustela putorius furo	ENSMPUG00000013714	1 retrocopy	retro_mputfur_657,
Ochotona princeps	ENSOPRG00000012401	2 retrocopies	retro_opri_356, retro_opri_474 ,
Pteropus vampyrus	ENSPVAG00000002909	3 retrocopies	retro_pvam_779, retro_pvam_847, retro_pvam_873,