RetrogeneDB ID: retro_mmul_2592

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:68892846..68893627(-)
• Located in intron of: ENSMMUG00000017753

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNOT7
• Ensembl ID: ENSMMUG00000001873
• Aliases: None
• Description: CCR4-NOT transcription complex subunit 7 [Source:RefSeq peptide;Acc:NP_001253776]

Sequence

>retro_mmul_2592
ATGCCAGCAGCAACTGTGGATTATAGCCAAAGAATTTGTGAAGTTTGGGCTTGCAACGTGGATGAAGAGATGATGAAAAT
TCGTCAAGTTATCCAAAAATATAATTACATTGCTATGGACACTTGAGTTTCCAGGTGTGGTTGCAAGACCCACTGGGGAA
TTCAGGAGCAATGCTGACTATCAATACCAACTATTGCGGTGTAATGTAGACTTGCTAAAGATAATTCAGCTAGGACTGAC
ATTTATGAATGAGCAAGGAGAATACCCTCCAGGAACTTCAACTTGGCAGTTTAATTTTAAATTTAATTTGACGGAGGACA
TGTATGCCCAGGACTCTATAGAGCTACTAACAACACGTGGTATCCGGTTTAAAAAACATGATGAGGAAGGAATTGAGACC
CAGTACTTTGTAGAACTTCTTATGACTTCAGGAGTGGTCCTCTGTGAAGGGGTCAAATGGTTGTCATTTCATAGCAGTTA
CAACTTTGGCTATTTAATCAAAATCCTGACCAACTCTAACTTGCCTGAAGAAGAACTTGACTTCTTTGAGATCCTTCCAT
TGTTTTTACCTGCCATTTATGATGTGAAGTACCTCATGAAGAGCTGCAAAAATCTCAAAGATGGATTACAGGAGGTGGCA
GAACAGTTAAAACTGGAATAGATAGGACCACAACATCAGGCAGGATCTAATTCATTGCTCACAGGAATGGCCTTTTTCAA
AATGAGAGAAATGTTCTTTGAAGGTCATATTGATAATGACAAATATTGTGGTCATTTGTAT

Alignment

ORF - retro_mmul_2592 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.19 %
• Parental protein coverage: 91.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPAATVDHSQRICEVWACNLDEEMKKIRQVIRKYNYVAMDT-EFPGVVARPIGEFRSNADYQYQLLRCNV
          MPAATVD.SQRICEVWACN.DEEM.KIRQVI.KYNY.AMDT.EFPGVVARP.GEFRSNADYQYQLLRCNV
Retrocopy MPAATVDYSQRICEVWACNVDEEMMKIRQVIQKYNYIAMDT>EFPGVVARPTGEFRSNADYQYQLLRCNV

Parental  DLLKIIQLGLTFMNEQGEYPPGTSTWQFNFKFNLTEDMYAQDSIELLTTSGIQFKKHEEEGIETQYFAEL
          DLLKIIQLGLTFMNEQGEYPPGTSTWQFNFKFNLTEDMYAQDSIELLTT.GI.FKKH.EEGIETQYF.EL
Retrocopy DLLKIIQLGLTFMNEQGEYPPGTSTWQFNFKFNLTEDMYAQDSIELLTTRGIRFKKHDEEGIETQYFVEL

Parental  LMTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEILRLFFPVIYDVKYLMKSCKNLKGGL
          LMTSGVVLCEGVKWLSFHS.Y.FGYLIKILTNSNLPEEELDFFEIL.LF.P.IYDVKYLMKSCKNLK.GL
Retrocopy LMTSGVVLCEGVKWLSFHSSYNFGYLIKILTNSNLPEEELDFFEILPLFLPAIYDVKYLMKSCKNLKDGL

Parental  QEVAEQLELERIGPQHQAGSDSLLTGMAFFKMREMFFEDHIDDAKYCGHLY
          QEVAEQL.LE.IGPQHQAGS.SLLTGMAFFKMREMFFE.HID..KYCGHLY
Retrocopy QEVAEQLKLE*IGPQHQAGSNSLLTGMAFFKMREMFFEGHIDNDKYCGHLY

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	0.00 RPM	52.33 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	34.43 RPM
SRP007412_cerebellum	0.00 RPM	48.75 RPM
SRP007412_heart	0.00 RPM	20.02 RPM
SRP007412_kidney	0.00 RPM	34.15 RPM
SRP007412_liver	0.04 RPM	13.02 RPM
SRP007412_testis	0.00 RPM	45.95 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2592 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2592 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2592 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4851
Pongo abelii	retro_pabe_3771

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000677	4 retrocopies	retro_chof_1431, retro_chof_1581, retro_chof_822, retro_chof_963,
Callithrix jacchus	ENSCJAG00000011795	1 retrocopy	retro_cjac_720,
Felis catus	ENSFCAG00000000591	1 retrocopy	retro_fcat_1889,
Homo sapiens	ENSG00000198791	2 retrocopies	retro_hsap_211, retro_hsap_4851,
Macaca mulatta	ENSMMUG00000001873	1 retrocopy	retro_mmul_2592 ,
Mustela putorius furo	ENSMPUG00000017972	1 retrocopy	retro_mputfur_1596,
Nomascus leucogenys	ENSNLEG00000002489	2 retrocopies	retro_nleu_1860, retro_nleu_2373,
Oryctolagus cuniculus	ENSOCUG00000014589	1 retrocopy	retro_ocun_118,
Otolemur garnettii	ENSOGAG00000006324	2 retrocopies	retro_ogar_1883, retro_ogar_505,
Pongo abelii	ENSPPYG00000018385	2 retrocopies	retro_pabe_3771, retro_pabe_428,
Sarcophilus harrisii	ENSSHAG00000011828	2 retrocopies	retro_shar_103, retro_shar_631,
Ictidomys tridecemlineatus	ENSSTOG00000009175	2 retrocopies	retro_itri_1729, retro_itri_1730,