RetrogeneDB ID: retro_ogar_2320

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873611.1:504269..505371(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COLEC12
• Ensembl ID: ENSOGAG00000003364
• Aliases: None
• Description: collectin sub-family member 12 [Source:HGNC Symbol;Acc:16016]

Sequence

>retro_ogar_2320
ATTCAGGAAGGAATATAAGGTACCAGATGTAAAAATAACTGAGCACTCAAGTTTTCTATCATATTATTATACATTTTTTA
TGCCTTGATAACAATCACAGTAGCCATTTGAGATACAAAATTTTGGAGAAAATGAACAATGTCACAGGTGGTAGTGAGAC
ATCTCACCAAATCTATGATGACAAACTCACAGGAGAAGAAAGTGACCTGAAAACATTAGGGGATCAAGCAGGAAAGAAAG
CTATAAGCACCAATGCAGAACTTCCCATCTTCAAATCAGATATTCTGGACCTTCATCAGTAACTTTGTGAGGTGACAGGG
AGTACCAGCAAGGACAAAGATATGCCAGGGAGGTTACAGGCCAGTGGGGATGAACTGGTGGACAGGCAGTCAACTAAGAG
AACTTTGGAGAATAGTTCTTTCCTCATCACCACTATAAATAAAACCTTCTGGGTATATAATGGTCATGCCATAAACCTGC
CACAAGATACCAGCGTGCTCCAAGGCAACCTGCAGAATCAAATATGTTCTTAAATGTGGTCCCTGTGAACCTCGACAACC
TGAACCTGACCTAGGCGCAGCACAGGAACCTCATCACTAATCTGCAACTGTCTGCAGATTATATAATCAGGCTATCCAGC
AAATCAAGAATGACTTCCAAAAGCTGCTGCAGATTTTCCTTCAAACCAAAAAGGACAGCAATAGGCTGAAAGAGAAAAGA
CAGAGCTTCCAGGCACCACCTACCCACAACTTTGACTTGGCCAAAGCCAACACCATCACCCTGGAGGATCTGAACAGCCA
GCTCAACTCATTCACAAATCAGATAGACAACATCACCACTACCTCTCAGACCAATGAACAGAACCTGAAAGTTCTTCAGA
CTTACACAGGATGTGGAGAATAGAACAGCCAAGTTCAGGCAACTGGAGGAATGCTTCCAGCTCTTTGAGACAGATATTAT
GAACATCATTAGCAATTTCAGTTACACACTCCACTACCTGCAGTGCCTGACCAGTGATCTGAATGAAGTCAGGACCTTGT
GCACCAATACTCAAACCAAATGCTCTGATGACTTGACCTCCTTGAGTAATACATGGGCTAAC

Alignment

ORF - retro_ogar_2320 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.68 %
• Parental protein coverage: 51.39 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  IQEGTQCTKCKNNWALKFSIILLYILCALLTITVAI-LGYKVVEKMDNVTGGMETSRQTYDDKLTAVESD
          IQEG...T.CKNN.ALKFSIILLYI..AL.TITVAI.L.YK..EKM.NVTGG.ETS.Q.YDDKLT..ESD
Retrocopy IQEGI*GTRCKNN*ALKFSIILLYIFYALITITVAI<LRYKILEKMNNVTGGSETSHQIYDDKLTGEESD

Parental  LKKLGDQTGKKAISTNSELSTFRSDILDLRQQLREITEKTSKNKDTLEKLQASGDALVDRQSQLKETLEN
          LK.LGDQ.GKKAISTN.EL..F.SDILDL.Q.L.E.T..TSK.KD....LQASGD.LVDRQS..K.TLEN
Retrocopy LKTLGDQAGKKAISTNAELPIFKSDILDLHQ*LCEVTGSTSKDKDMPGRLQASGDELVDRQS-TKRTLEN

Parental  NSFLITTVNKTLQAYNGYVTNLQQDTSALQGNLQSQMYS-HNVVIMSLNNLNLTQVQQRNLITNLQRSVD
          .SFLITT.NKT...YNG...NL.QDTS.LQGNLQ.Q..S..NVV...L.NLNLT..Q.RNLITNLQ.S.D
Retrocopy SSFLITTINKTFWVYNGHAINLPQDTSVLQGNLQNQICS<LNVVPVNLDNLNLT*AQHRNLITNLQLSAD

Parental  DT-SQAIQRIKNDFQNLQQVFLQAKKDTDWLKEKVQSLQTLAANNSALAKANNDTLEDMNSQLNSFTGQM
          ....QAIQ.IKNDFQ.L.Q.FLQ.KKD...LKEK.QS.Q.....N..LAKAN..TLED.NSQLNSFT.Q.
Retrocopy YI<NQAIQQIKNDFQKLLQIFLQTKKDSNRLKEKRQSFQAPPTHNFDLAKANTITLEDLNSQLNSFTNQI

Parental  DNITTISQANEQNLKDLQ-DSHK-DAENRTAIKFNQLEERFQLFETDIVNIISNISYTAHHLRTLTSNLN
          DNITT.SQ.NEQNLK.LQ.D.H..D.ENRTA.KF.QLEE.FQLFETDI.NIISN.SYT.H.L..LTS.LN
Retrocopy DNITTTSQTNEQNLKVLQ<DLHR<DVENRTA-KFRQLEECFQLFETDIMNIISNFSYTLHYLQCLTSDLN

Parental  EVRTTCTDTLTKHTDDLTSLNNTLAN
          EVRT.CT.T.TK..DDLTSL.NT.AN
Retrocopy EVRTLCTNTQTKCSDDLTSLSNTWAN

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_2320 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000146	4 retrocopies	retro_cjac_3363, retro_cjac_3473, retro_cjac_3628, retro_cjac_3630,
Otolemur garnettii	ENSOGAG00000003364	1 retrocopy	retro_ogar_2320 ,