RetrogeneDB ID: retro_mmul_340

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:86305913..86306279(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000029420
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RPL31
• Ensembl ID: ENSMMUG00000009873
• Aliases: None
• Description: None

Sequence

>retro_mmul_340
ATGGCTCCCGCAAAGAAGGGTGGCGAGAAGAAAAAGGGCCGTTCTGCCATCAACAAGGTGGTGACCCGAGAATACACCAT
CAACATTCACAAGTGCATCCATGGAGTGGGCTTCAAGAAGCATGCCCCTCGGGCACTCAAAGAGATTCGGAAATTTGCCA
TGAAGGAGATGGGAACTCCAGATGTGCGCCTTGATACAAGGCTCAACAAAGCTGTCTGGCCCAAAGGAATAAGGAATGTC
CCATACCGAATCCGTGTGCGGCTGTCCAGAAAACGTAATGAGGATGAAGATTCACCAAATAAGTTCTATACTTTGGTTAC
CTATGTACCTGTTACCACTTTCAAAAGTAAGTTCTCCATCCCATAA

Alignment

ORF - retro_mmul_340 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.04 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPAKKGGEKKKGRSAINEVVTREYTINIHKRIHGVGFKKRAPRALKEIRKFAMKEMGTPDVRIDTRLNK
          MAPAKKGGEKKKGRSAIN.VVTREYTINIHK.IHGVGFKK.APRALKEIRKFAMKEMGTPDVR.DTRLNK
Retrocopy MAPAKKGGEKKKGRSAINKVVTREYTINIHKCIHGVGFKKHAPRALKEIRKFAMKEMGTPDVRLDTRLNK

Parental  AVWAKGIRNVPYRIRVRLSRKRNEDEDSPNKLYTLVTYVPVTTFKSKFSIP
          AVW.KGIRNVPYRIRVRLSRKRNEDEDSPNK.YTLVTYVPVTTFKSKFSIP
Retrocopy AVWPKGIRNVPYRIRVRLSRKRNEDEDSPNKFYTLVTYVPVTTFKSKFSIP

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	1.01 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	66.08 RPM
SRP007412_cerebellum	0.26 RPM	2.26 RPM
SRP007412_heart	0.00 RPM	1.71 RPM
SRP007412_kidney	0.00 RPM	1.29 RPM
SRP007412_liver	0.00 RPM	0.75 RPM
SRP007412_testis	0.04 RPM	0.57 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_340 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_340 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_340 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 111 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000007914	1 retrocopy	retro_acar_168,
Homo sapiens	ENSG00000071082	45 retrocopies	retro_hsap_1026, retro_hsap_1056, retro_hsap_1075, retro_hsap_1102, retro_hsap_1118, retro_hsap_1150, retro_hsap_1217, retro_hsap_1269, retro_hsap_1345, retro_hsap_1527, retro_hsap_1691, retro_hsap_1856, retro_hsap_1865, retro_hsap_1993, retro_hsap_1998, retro_hsap_2215, retro_hsap_2246, retro_hsap_2388, retro_hsap_2470, retro_hsap_2510, retro_hsap_2610, retro_hsap_2615, retro_hsap_2627, retro_hsap_2839, retro_hsap_2921, retro_hsap_2959, retro_hsap_3108, retro_hsap_3325, retro_hsap_3471, retro_hsap_3472, retro_hsap_3525, retro_hsap_3731, retro_hsap_3777, retro_hsap_3788, retro_hsap_3899, retro_hsap_3965, retro_hsap_4070, retro_hsap_4210, retro_hsap_461, retro_hsap_4693, retro_hsap_506, retro_hsap_548, retro_hsap_677, retro_hsap_794, retro_hsap_831,
Gorilla gorilla	ENSGGOG00000006432	24 retrocopies	retro_ggor_1047, retro_ggor_113, retro_ggor_1442, retro_ggor_169, retro_ggor_1811, retro_ggor_1839, retro_ggor_192, retro_ggor_1971, retro_ggor_21, retro_ggor_2132, retro_ggor_2383, retro_ggor_2541, retro_ggor_2547, retro_ggor_2625, retro_ggor_2820, retro_ggor_442, retro_ggor_583, retro_ggor_655, retro_ggor_834, retro_ggor_84, retro_ggor_849, retro_ggor_874, retro_ggor_88, retro_ggor_997,
Latimeria chalumnae	ENSLACG00000013603	1 retrocopy	retro_lcha_94,
Macropus eugenii	ENSMEUG00000000963	8 retrocopies	retro_meug_1083, retro_meug_1433, retro_meug_1731, retro_meug_1741, retro_meug_198, retro_meug_418, retro_meug_588, retro_meug_649,
Myotis lucifugus	ENSMLUG00000002507	21 retrocopies	retro_mluc_1072, retro_mluc_1135, retro_mluc_1239, retro_mluc_1301, retro_mluc_1406, retro_mluc_1470, retro_mluc_1666, retro_mluc_1678, retro_mluc_1896, retro_mluc_1913, retro_mluc_2028, retro_mluc_2124, retro_mluc_2126, retro_mluc_269, retro_mluc_303, retro_mluc_463, retro_mluc_767, retro_mluc_782, retro_mluc_914, retro_mluc_922, retro_mluc_997,
Macaca mulatta	ENSMMUG00000009873	1 retrocopy	retro_mmul_340 ,
Monodelphis domestica	ENSMODG00000001704	5 retrocopies	retro_mdom_1052, retro_mdom_1464, retro_mdom_1674, retro_mdom_1720, retro_mdom_1818,
Nomascus leucogenys	ENSNLEG00000014444	2 retrocopies	retro_nleu_47, retro_nleu_530,
Sarcophilus harrisii	ENSSHAG00000011706	3 retrocopies	retro_shar_190, retro_shar_285, retro_shar_721,