RetrogeneDB ID: retro_opri_482

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_135:500975..502487(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SP3
• Ensembl ID: ENSOPRG00000005517
• Aliases: None
• Description: Sp3 transcription factor [Source:HGNC Symbol;Acc:11208]

Sequence

>retro_opri_482
ACAGGTGATTTGGCTTCTACACAGTTAGGAGGAGCACCAAATCGATGGGAGGTTTTGTCAGCCACACCTACAACTATAAA
AGATGAAGCTGGTAATCTAGTGCAGATTCCAAGTGCTGCTACTTCGAGTGGGCAGTATGTCCTTCCCCTTCAGAATTTGC
AGAATCAACAAATATTTTCAGTTGCACCAGGATCAGATTCATCAAATGGTACCGTGTCCAATGTTCAATATCAAGTAATA
CCACAGATTCAGTCCACAGATGGTCAGCAGGTCCAGATTGGTTTCACAGGCTCTTCAGATAATGGGGGTATAAATCAAGA
AAGCAGTCAAATTCAGATCATTCCTGGCTCTAATCAGACCTTACTTGCCTCTGGAACGCCTCCTGCTAATATCCAGAATC
TCATACCACAGACTGGTCAAGTCCAGGTTCAGGGAGTTGCAATTGGTGGTTCTTCTTTTCCTGGCCAAACCCAAGTAGTT
GCTAATGTGCCTCTCGGTCTGCCAGGAAATATTACCTTTGTACCAATCAATAGTGTTGATCTAGATTCTTTGGGACTCTC
GGGCAGTTCTCAGACAATGACTGCAGGCATCAATGCCGATGGACATTTGATAAACACAGGACAAGCTATGGATAGTTCAG
ACAATTCAGAAAGGACTGGTGAACGGGTTTCTCCTGATATTAATGAAACTAACACTGATACAGATTTATTTGTGCCAACG
TCCTCTTCATCACAGTTGCCTGTTACGATAGATAGTACAGGTATATTACAACAAAACACAAATAGCTTGACTACTTCTAG
TGGGCAAGTTCATTCTTCAGATCTTCAGGGAAATTATATCCAGTCGCCTGTTTCTGAAGAGACACAGGCTCAGAATATTC
AGGTTTCTATGGCACAGCCTGTTGTACAACATCTACAACTTCAAGAGTCTCAGCAGCCAACCAGTCAAGCCCAAATTGTG
CAAGGTATTACACCACAGATAATCCATGGTGTGCAAGCCAGTGGTCAGAATATATCACAACAAATTTTGCAAAATCTTCA
GTTGCAGCTGAATCCTGGAACCTTTTTAATTCAGGCACAGACAAGTGACCCCTTCTGGACAGATAACTTGGCAGACATTA
CAAGTACAAGGAGTCCAGAACTTGCAGAATTTGCAAATACAGAATATGGCTGCCGAACAGATAACTTTGACACCTGTTTA
GACACTCACATTTGGTCAAGTTGCAGCAGGTGGAGCCTTGACTTCAACTCCAGTTAGTCTGAGCACTGCTCAGTTGCCAA
ATCTACAGACAGTTACAGTAAACTCTATAGATTCTACTGAGATTCAGCTGCATTCAAGAGAGAATGCTGACAGTCTGCAG
ATATTAGAATCAAGGAAGAAGAGCCTGAACCTGAAGAGTGGCAGCTCAGTGGTGATTCTACATTGAATCCCAATGATCTA
ACACACTTAAGAGTGCAGGTGGTAGATGAAGAAGGGGACCAACAATATCAAGGAAAAAGACTTTGGAGGGTA

Alignment

ORF - retro_opri_482 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.22 %
• Parental protein coverage: 64.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TGDLASTQLGGAPNRWEVLSATPTTIKDEAGNLVQIPSAATSSGQYVLPLQNLQNQQIFSVAPGSDSSNG
          TGDLASTQLGGAPNRWEVLSATPTTIKDEAGNLVQIPSAATSSGQYVLPLQNLQNQQIFSVAPGSDSSNG
Retrocopy TGDLASTQLGGAPNRWEVLSATPTTIKDEAGNLVQIPSAATSSGQYVLPLQNLQNQQIFSVAPGSDSSNG

Parental  TVSNVQYQVIPQIQSTDGQQVQIGFTGSSDNGGINQESSQIQIIPGSNQTLLASGTPPANIQNLIPQTGQ
          TVSNVQYQVIPQIQSTDGQQVQIGFTGSSDNGGINQESSQIQIIPGSNQTLLASGTPPANIQNLIPQTGQ
Retrocopy TVSNVQYQVIPQIQSTDGQQVQIGFTGSSDNGGINQESSQIQIIPGSNQTLLASGTPPANIQNLIPQTGQ

Parental  VQVQGVAIGGSSFPGQTQVVANVPLGLPGNITFVPINSVDLDSLGLSGSSQTMTAGINADGHLINTGQAM
          VQVQGVAIGGSSFPGQTQVVANVPLGLPGNITFVPINSVDLDSLGLSGSSQTMTAGINADGHLINTGQAM
Retrocopy VQVQGVAIGGSSFPGQTQVVANVPLGLPGNITFVPINSVDLDSLGLSGSSQTMTAGINADGHLINTGQAM

Parental  DSSDNSERTGERVSPDINETNTDTDLFVPTSSSSQLPVTIDSTGILQQNTNSLTTSSGQVHSSDLQGNYI
          DSSDNSERTGERVSPDINETNTDTDLFVPTSSSSQLPVTIDSTGILQQNTNSLTTSSGQVHSSDLQGNYI
Retrocopy DSSDNSERTGERVSPDINETNTDTDLFVPTSSSSQLPVTIDSTGILQQNTNSLTTSSGQVHSSDLQGNYI

Parental  QSPVSEETQAQNIQVSMAQPVVQHLQLQESQQPTSQAQIVQGITPQIIHGVQASGQNISQQILQNLQLQL
          QSPVSEETQAQNIQVSMAQPVVQHLQLQESQQPTSQAQIVQGITPQIIHGVQASGQNISQQILQNLQLQL
Retrocopy QSPVSEETQAQNIQVSMAQPVVQHLQLQESQQPTSQAQIVQGITPQIIHGVQASGQNISQQILQNLQLQL

Parental  NPGTFLIQAQT-VTPSGQITWQTLQVQGVQNLQNLQIQNMAAEQITLTPV-TLTFGQVAAGGALTSTPVS
          NPGTFLIQAQT.VTPSGQITWQTLQVQGVQNLQNLQIQNMAAEQITLTPV.TLTFGQVAAGGALTSTPVS
Retrocopy NPGTFLIQAQT>VTPSGQITWQTLQVQGVQNLQNLQIQNMAAEQITLTPV*TLTFGQVAAGGALTSTPVS

Parental  LSTAQLPNLQTVTVNSIDSTEIQLHSRENADS-PADIRIKEEEPDPEEWQLSGDSTLNTNDLTHLRVQVV
          LSTAQLPNLQTVTVNSIDSTEIQLHSRENADS..ADIRIKEEEP.PEEWQLSGDSTLN.NDLTHLRVQVV
Retrocopy LSTAQLPNLQTVTVNSIDSTEIQLHSRENADS<SADIRIKEEEPEPEEWQLSGDSTLNPNDLTHLRVQVV

Parental  DEEGDQQHQEGKRLRRV
          DEEGDQQ.Q.GKRL.RV
Retrocopy DEEGDQQYQ-GKRLWRV

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_482 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ochotona princeps	ENSOPRG00000005517	1 retrocopy	retro_opri_482 ,