RetrogeneDB ID: retro_ogar_2812

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873666.1:1132252..1132966(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPDYC
• Ensembl ID: ENSOGAG00000015020
• Aliases: None
• Description: speedy/RINGO cell cycle regulator family member C [Source:HGNC Symbol;Acc:32681]

Sequence

>retro_ogar_2812
CAAGGAGGAGGCACTGGGTTTCTCCATTCCCAGTAGCACAAGGAACTCCAGGCCTTCCTCAGGCTTCTGGAGGACAGCTT
TGCCCAGGAATTCCTCTCCAAAGACCTGTGCTTCTGGATTTTGGATAAGTATCTCCTGGCCATGGTGCTGGTCTACTTAT
AGTGCACCCACCTGAAGCTCAGCGGGTATACCCACAGCAGCCTGTTCCTGGCACTGTACCTTGCAAATGACATGGAGGAG
GATCTGGGAGAGCCCAAATGTGAGATTTTCCCCATGGGCCCTGGGAGAAGATTGGTACCTTCAGGTGGCAAAATTCCTGC
ACCAGAGGGACAAGCTGGGGGCACAGACGAGCTTTCAGGCAGTGGGGAGCCGCCAGTGCTGTGAGGAGGTCATGGTCATG
GAGCCGTCCCACTGGGCTTGGACTTGGGAGCAGTGCCTCCACTATGGCTAGGTTCAGAGGGGCTGTCCACAGGTCCAAGG
CCACTTCCCTCCTGGGCCCTGGCCTCTCACCACCCCATCATTCCCTCTGAGGCTCGTCCCAGCACCACAGCCACCACCAT
TCTTTGTCTGCATTATCCAAGTGCCCAGCCCTGACCTCAGAGTGCCATCATCCTCCTTCCCAAAATTATCTCTCAGGAGT
CAAAAAAACCCTGGGGTGGGAAGTTTCTCATCATTTTGTACCCTCAGATACAGCTAGAACCAGGCACCTACACC

Alignment

ORF - retro_ogar_2812 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.5 %
• Parental protein coverage: 87.78 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QGGGTGFLHSRQHKELQAFLSLLEDSLIQEFLSKDPCFWISDKYLLAMVLVYFQRAHLKLSEYTHSSLFL
          QGGGTGFLHS..HKELQAFL.LLEDS..QEFLSKD.CFWI.DKYLLAMVLVY....HLKLS.YTHSSLFL
Retrocopy QGGGTGFLHSQ*HKELQAFLRLLEDSFAQEFLSKDLCFWILDKYLLAMVLVYL*CTHLKLSGYTHSSLFL

Parental  ALYLANDMEEDLEEPKCEIF-PWALGEDWYLQVGKFLHQRDKLWARMGFQAVVSRQCCEEIMAMEPSHWA
          ALYLANDMEEDL.EPKCEIF.PWALGEDWYLQV.KFLHQRDKL.A...FQAV.SRQCCEE.M.MEPSHWA
Retrocopy ALYLANDMEEDLGEPKCEIF>PWALGEDWYLQVAKFLHQRDKLGAQTSFQAVGSRQCCEEVMVMEPSHWA

Parental  WTRERRPHHGGVQRGCPQVPGRFP-RGPGLSPPHCSLCGSSQHHSHHHPLPALSKCPALTSECHHPHSQN
          WT.E...H.G.VQRGCPQV.G.FP..GPGLSPPH.SL.GSSQHHSHHH.L.ALSKCPALTSECHHP.SQN
Retrocopy WTWEQCLHYG*VQRGCPQVQGHFP>LGPGLSPPHHSL*GSSQHHSHHHSLSALSKCPALTSECHHPPSQN

Parental  YLSGV-KNPWGGEFLIILPPQMQLEPGTYT
          YLSGV.K.PWGG.FLIIL.PQ.QLEPGTYT
Retrocopy YLSGV>KKPWGGKFLIILYPQIQLEPGTYT

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_2812 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 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002403	2 retrocopies	retro_cjac_1136, retro_cjac_1851,
Monodelphis domestica	ENSMODG00000010068	3 retrocopies	retro_mdom_1043, retro_mdom_1348, retro_mdom_1695,
Otolemur garnettii	ENSOGAG00000015020	1 retrocopy	retro_ogar_2812 ,