RetrogeneDB ID: retro_ogar_941

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873531.1:4586803..4587841(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RFC2
• Ensembl ID: ENSOGAG00000014927
• Aliases: None
• Description: replication factor C (activator 1) 2, 40kDa [Source:HGNC Symbol;Acc:9970]

Sequence

>retro_ogar_941
GCTGAAATGGAGGAGCAGGGGAGCAGCGGTGGTGCGACCGATTGGGGGATCCAGGACCCTGCTGCTGCCCCCAGCAAGGC
CTCCAGCAGTGCCGGCCACTATGAGCTGCCAGGGGCTGAAAAATATAGACCAGTAAAGCTGAATGAAGTTGCTGGGAATG
AAGACACTGTGAGCAGGCTGGAGATCTTTGCAAGAGAAGGGAATGTGCCCAATATCATCATCACTGGCCCCCCAGGAACT
GGCAAAGCTACAAACGTCCTGTGTTTGGCACAAGGCTTGCTGGGCCCAGCAATGAATGATGCTGTCTTGGAACTCAGTGC
TTCAAATGATAGGGGCATTGATGCTGTGAATAAAATCAAAATGTTTGCTCAACAAAGAGTCAGGCTTCCCAAAGGTCGAC
ACAAGATCATCATCTTGGATGAAGCAGACAGCATGACTGATGGAGCCCAGCAAGCCTTGAGGAGAACCATGGAGATCTAC
TCTAAAAGGACTCGCTTTGTGCTTGCTTGTAATGCTTTTGATAAGATCATGGAGCCCATCCAGCCCCGGCATGCCATCCT
CTGCTACACCAAGCTGACTGATGCCCAGATATTGGCATGGCTGCTAAACATAATCAAGAAGGAGAAGGTGCCATCGATTG
ATGATGGCCTGGAAGCCATCATTCTCATAGCCCAGGGAGACATGTGGCAGGCATTGAACAACTTGCAGTCCACTTTCTCA
GGATTTGGCTTCATCAACAGTGAGAATGTATTCAAGGTCTGTGATGAGCCCCACCCTCTACTCATGAAGGAGAAGATCCA
GCATTGTGTGGATGCCAACATTGATGAGGCCTACAAGATTCTTGCTCACCTGTGGCACCTGGGCTATTCACCAGAAGATG
TCATTGGCAATACCTTTTGAGTATGTAAAACGTTCCAAATGGCAGAATACTTGAAACTGGAGTTTATTAAGGAAATTGGA
TACACTCATAAGAAAGTAGCAGAAGGAGTGAACTCCCTTCTGCAGATGGCAGGGCTCCTAGCCAGGCTGTATCAGAAG

Alignment

ORF - retro_ogar_941 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.61 %
• Parental protein coverage: 98.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AEMEELGSCGGATDRGIQDTAAAPSKASSSAGHYELPWVEKYRPIKLNEVVGNEDTVSRLEVFAREGNVP
          AEMEE.GS.GGATD.GIQD.AAAPSKASSSAGHYELP..EKYRP.KLNEV.GNEDTVSRLE.FAREGNVP
Retrocopy AEMEEQGSSGGATDWGIQDPAAAPSKASSSAGHYELPGAEKYRPVKLNEVAGNEDTVSRLEIFAREGNVP

Parental  NIIIAGPPGTGKTTSILCLARALLGPAMKDAVLELNASNDRGIDVVRNKIKMFAQQKVTLPKGRHKIIIL
          NIII.GPPGTGK.T..LCLA..LLGPAM.DAVLEL.ASNDRGID.V.NKIKMFAQQ.V.LPKGRHKIIIL
Retrocopy NIIITGPPGTGKATNVLCLAQGLLGPAMNDAVLELSASNDRGIDAV-NKIKMFAQQRVRLPKGRHKIIIL

Parental  DEADSMTDGAQQALRRTMEIYSKTTRFALACNASDKIIEPIQSRCAVLRYTKLTDAQILARLLNVIEKEK
          DEADSMTDGAQQALRRTMEIYSK.TRF.LACNA.DKI.EPIQ.R.A.L.YTKLTDAQILA.LLN.I.KEK
Retrocopy DEADSMTDGAQQALRRTMEIYSKRTRFVLACNAFDKIMEPIQPRHAILCYTKLTDAQILAWLLNIIKKEK

Parental  VPYTDDGLEAIIFTAQGDMRQALNNLQSTFSGFGFINSENVFKVCDEPHPLLVKEMIQHCVDANIDEAYK
          VP..DDGLEAII..AQGDM.QALNNLQSTFSGFGFINSENVFKVCDEPHPLL.KE.IQHCVDANIDEAYK
Retrocopy VPSIDDGLEAIILIAQGDMWQALNNLQSTFSGFGFINSENVFKVCDEPHPLLMKEKIQHCVDANIDEAYK

Parental  ILAHLWHLGYSPEDVIGNIFRVCKTFQMAEYLKLEFIKEIGYTHMKVAEGVNSLLQMAGLLARLCQK
          ILAHLWHLGYSPEDVIGN.F.VCKTFQMAEYLKLEFIKEIGYTH.KVAEGVNSLLQMAGLLARL.QK
Retrocopy ILAHLWHLGYSPEDVIGNTF*VCKTFQMAEYLKLEFIKEIGYTHKKVAEGVNSLLQMAGLLARLYQK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_941 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003985	1 retrocopy	retro_cjac_12,
Otolemur garnettii	ENSOGAG00000014927	1 retrocopy	retro_ogar_941 ,