RetrogeneDB ID: retro_mmul_2529

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:118161568..118162699(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.9547
• Ensembl ID: ENSMMUG00000019904
• Aliases: CCNI, cyclin-I
• Description: cyclin I [Source:RefSeq peptide;Acc:NP_001182374]

Sequence

>retro_mmul_2529
ATGAAGTTTCCAGGGCCTTTGGAAAACTAGAGATTGTCTTTCCTGTTGGAAAAGGCAATCACTAGGGAAGCGCAGATGTG
GAAAGTGAATGTGCGGAAAATGCCTTCAAATCAGAGTATTTCTCCATCCCAGAGAGATGAAGTAATTCAATGGCTGGCCA
AACTCAAGTACCAATTCAACCTTTACCCAGAAACATTTGCTCTGGCTGGCAGTCTTTTGGACAGGTTTTTAGCTACCGTA
AAGGCTCATCCGATATACTTGAGTTGTATTGCAATCAGCTGTTTTTTCCTAGCTGCCAAGACTGTTGAGGAAGATGAGAG
AATTCCAGTACTAAAGGTATTGGCAAGAGACAGTTTCTGTGGATGTTCCTCATCTGAAATTTTGAGAATGGAGAGAATTA
TTCTGGATAAGTTGAATTGGGATCTTCACACAGCCACACCATTGGATTGTCTTCATATTTTCCATGCTATTGCGGTGTCA
ACTAGGCCTCAGTTACTTTTCAGTTTGCCCAAATTGAGCCCATCTCAACATTTGGCAGTCCTTACCAAGCAACTACTTCA
CTGTATGGCCTGCAACCAACTTCTGCAATTCAGAGGATCCATGCTTGCTCTGGCCATGGTTAGTCTGGAAATGGAGAAAC
TTATTCCTGATTGGCTTTCTCTTACAATTGAACTGCTTCGGAAAGCACAGATGGATAGCTCCCAGTTGATCCACTGTCAG
GAGCTTGTGGCACATCACCTTTCTACTCTGTAGTCTTCCCTGCCTCTAAATTCCGTTTATGTCTACCGTCCCCTCAAGCA
CACCCTGGTGACCTGTGACAAAGGAGTGTTCAGATTACATCCCTCCTCTGTCCCAGGCCCAGACTTCTCCAAGGACAACA
GCAAGCCAGAAGTGCCAGTCAGAGGTACAGCAGCTTTTTACCATCATCTCCCAGCTGCCAGTGGGTGCAAGCAGACCTCT
GCTAAACGCAAAGTAGAGGAAATGGAAGGGGATGACTTCTATGATGGAATCAAACGGCTCTATAATGAAGATAATGTCTC
AGAAAATGTGGGTTCTGTGTGTGGCACTGACTTATCAAGACAAGAGGGACATGCTTCCCCTTGTCCACCTTTGCAGCCTG
TTTCTGTCATG

Alignment

ORF - retro_mmul_2529 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.08 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKFPGPLENQRLSFLLEKAITREAQMWKVNVRKMPSNQNVSPSQRDEVIQWLAKLKYQFNLYPETFALAS
          MKFPGPLEN.RLSFLLEKAITREAQMWKVNVRKMPSNQ..SPSQRDEVIQWLAKLKYQFNLYPETFALA.
Retrocopy MKFPGPLEN*RLSFLLEKAITREAQMWKVNVRKMPSNQSISPSQRDEVIQWLAKLKYQFNLYPETFALAG

Parental  SLLDRFLATVKAHPKYLSCIAISCFFLAAKTVEEDERIPVLKVLARDSFCGCSSSEILRMERIILDKLNW
          SLLDRFLATVKAHP.YLSCIAISCFFLAAKTVEEDERIPVLKVLARDSFCGCSSSEILRMERIILDKLNW
Retrocopy SLLDRFLATVKAHPIYLSCIAISCFFLAAKTVEEDERIPVLKVLARDSFCGCSSSEILRMERIILDKLNW

Parental  DLHTATPLDFLHIFHAIAVSTRPQLLFSLPKLSPSQHLAVLTKQLLHCMACNQLLQFRGSMLALAMVSLE
          DLHTATPLD.LHIFHAIAVSTRPQLLFSLPKLSPSQHLAVLTKQLLHCMACNQLLQFRGSMLALAMVSLE
Retrocopy DLHTATPLDCLHIFHAIAVSTRPQLLFSLPKLSPSQHLAVLTKQLLHCMACNQLLQFRGSMLALAMVSLE

Parental  MEKLIPNWLSLTIELLQKAQMDSSQLIHCRELVAHHLSTLQSSLPLNSVYVYRPLKHTLVTCDKGVFRLH
          MEKLIP.WLSLTIELL.KAQMDSSQLIHC.ELVAHHLSTL.SSLPLNSVYVYRPLKHTLVTCDKGVFRLH
Retrocopy MEKLIPDWLSLTIELLRKAQMDSSQLIHCQELVAHHLSTL*SSLPLNSVYVYRPLKHTLVTCDKGVFRLH

Parental  PSSVPGPDFSKDNSKPEVPVRGTAAFYHHLPAASGCKQTSAKRKVEEMEVDDFYDGIKRLYNEDNVSENV
          PSSVPGPDFSKDNSKPEVPVRGTAAFYHHLPAASGCKQTSAKRKVEEME.DDFYDGIKRLYNEDNVSENV
Retrocopy PSSVPGPDFSKDNSKPEVPVRGTAAFYHHLPAASGCKQTSAKRKVEEMEGDDFYDGIKRLYNEDNVSENV

Parental  GSVCGTDLSRQEGHASPCPPLQPVSVM
          GSVCGTDLSRQEGHASPCPPLQPVSVM
Retrocopy GSVCGTDLSRQEGHASPCPPLQPVSVM

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.56 RPM	287.41 RPM
SRP007412_brain_prefrontal_cortex	0.56 RPM	278.53 RPM
SRP007412_cerebellum	1.23 RPM	431.36 RPM
SRP007412_heart	0.24 RPM	107.82 RPM
SRP007412_kidney	0.35 RPM	136.15 RPM
SRP007412_liver	0.08 RPM	66.66 RPM
SRP007412_testis	0.23 RPM	64.04 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2529 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2529 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2529 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014768	1 retrocopy	retro_cjac_1311,
Echinops telfairi	ENSETEG00000000952	1 retrocopy	retro_etel_1137,
Loxodonta africana	ENSLAFG00000029218	1 retrocopy	retro_lafr_295,
Macaca mulatta	ENSMMUG00000000914	1 retrocopy	retro_mmul_879,
Macaca mulatta	ENSMMUG00000019904	1 retrocopy	retro_mmul_2529 ,
Mus musculus	ENSMUSG00000063015	2 retrocopies	retro_mmus_1211, retro_mmus_2730,
Tarsius syrichta	ENSTSYG00000009907	1 retrocopy	retro_tsyr_834,
Vicugna pacos	ENSVPAG00000011865	1 retrocopy	retro_vpac_197,