RetrogeneDB ID: retro_mmul_2389

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 9:30509463..30510294(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.3939
• Ensembl ID: ENSMMUG00000020928
• Aliases: None
• Description: None

Sequence

>retro_mmul_2389
AAGGAAGTGGCGCAGGTTCACAAGCGCGTAACCGGGCCAAAAAAAAAAAAAAAAAAAAAAAAAAACCGAGAACAACTTTC
TCCTGGAGTAGTCTATGTGCGCCACCCACCTAACCTACTTAAGGAAACCCAGATCCTTTCCTATTTCTCCCAGTGTGGCA
CTGTTACAAAGGTCAGACTGTCCAGAAAGAAAAGGACTGGATATAGCAAAGGCTATGCATTTGTGGAGTTTGAGTCTGAG
GATGTTGCCAAGATAGTTGCTGAAACAATGAACAACTACCTGTTTGGTGAAAGACCCTTGGAGTGTCGTTTCATGTCACC
TGAAAAAGTATAGAAAGAACTCTTTAAAGACTGGAATATTCCATTTAAGCAGCCATCATATCCATGAGTGAAATAGTATA
ATCAGAATCGGCACTTAACACAAAATCTACGAATGGAGGAGCGATTTTGAAAAAAAGAAAGATTACTCGGGAAGAAATTA
GCTTACAAAGGAATTGATTATGATTTTCCTTCTTTGATTTTACAGAAAACGGAAAGTATTTCAAAAATGAATCGTCGGAC
GTCTACAAAAGGCCAGGTTTTATGTTAGAAGAAGCAAAAGGTTTTAGGCACTCCTGACACTCCTGAGAAGACTGTGGATA
GCCATGGCCCCACACCGGTTTGTACATCAACATTTTTGGAGAGATGAAAATCTGAAGTGGCTGAAATGAATGATGATGAT
AAAGATAAGGAAATAGTTTTCAAACAGCCTGTATCCTGTGTAAAAGAAGAAATACAAGCAACTCAAACACCTACACATTC
ACAGAAAAAAAGTCATAGAAAAAGCAATCAG

Alignment

ORF - retro_mmul_2389 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.9 %
• Parental protein coverage: 94.54 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QEDAEFQKEVAQVRKRITQRKKQERLTSGVVYVGHLPNLLNETQIFSYFSQFGTVTRFRLSRSKRTGNSK
          .E.A...K.V.............E.L..GVVYV.H.PNLL.ETQI.SYFSQ.GTVT..RLSR.KRTG.SK
Retrocopy KEVAQVHKRVTGXXXXXXXXXXREQLSPGVVYVRHPPNLLKETQILSYFSQCGTVTKVRLSRKKRTGYSK

Parental  GYAFVEFESEDVAKIVAETMNNYLFGERLLECHFMPPEKVHKELFKDWNIPFKQPSHPSVKRYNRNRTLT
          GYAFVEFESEDVAKIVAETMNNYLFGER.LEC.FM.PEKV.KELFKDWNIPFKQPS.P.VK.YN.NR.LT
Retrocopy GYAFVEFESEDVAKIVAETMNNYLFGERPLECRFMSPEKV*KELFKDWNIPFKQPSYP*VK*YNQNRHLT

Parental  QKLRMEERFKKKERLLRKKLAKKGIDYDFPSLILQKTEGVSKTNRQTSTKGQVLRKKKKKVLGTPNVPEK
          Q.LRMEERF.KKERLL.KKLA.KGIDYDFPSLILQKTE..SK.NR.TSTKGQVL..KK.KVLGTP..PEK
Retrocopy QNLRMEERF*KKERLLGKKLAYKGIDYDFPSLILQKTESISKMNRRTSTKGQVLC*KKQKVLGTPDTPEK

Parental  TVDSQGPTPVCTPTFLERRKSEVAELNDDDKDNEIVFKEPISCVKEEIQETQTPTHSRKKRRRKSNQ
          TVDS.GPTPVCT.TFLER.KSEVAE.NDDDKD.EIVFK.P.SCVKEEIQ.TQTPTHS.KK..RKSNQ
Retrocopy TVDSHGPTPVCTSTFLER*KSEVAEMNDDDKDKEIVFKQPVSCVKEEIQATQTPTHSQKKSHRKSNQ

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	9.41 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	6.35 RPM
SRP007412_cerebellum	0.00 RPM	11.24 RPM
SRP007412_heart	0.00 RPM	7.36 RPM
SRP007412_kidney	0.00 RPM	9.74 RPM
SRP007412_liver	0.00 RPM	3.21 RPM
SRP007412_testis	0.34 RPM	10.63 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2389 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2389 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2389 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_553
Pan troglodytes	retro_ptro_415
Pongo abelii	retro_pabe_510

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019387	1 retrocopy	retro_btau_1516,
Choloepus hoffmanni	ENSCHOG00000002227	5 retrocopies	retro_chof_1061, retro_chof_1449, retro_chof_1735, retro_chof_236, retro_chof_2480,
Callithrix jacchus	ENSCJAG00000013386	1 retrocopy	retro_cjac_3076,
Dasypus novemcinctus	ENSDNOG00000005017	2 retrocopies	retro_dnov_1869, retro_dnov_2487,
Erinaceus europaeus	ENSEEUG00000008535	3 retrocopies	retro_eeur_530, retro_eeur_550, retro_eeur_91,
Homo sapiens	ENSG00000155438	5 retrocopies	retro_hsap_1077, retro_hsap_1596, retro_hsap_1609, retro_hsap_1611, retro_hsap_553,
Gorilla gorilla	ENSGGOG00000023498	4 retrocopies	retro_ggor_1213, retro_ggor_1923, retro_ggor_2225, retro_ggor_850,
Loxodonta africana	ENSLAFG00000030731	1 retrocopy	retro_lafr_500,
Microcebus murinus	ENSMICG00000015787	1 retrocopy	retro_mmur_990,
Myotis lucifugus	ENSMLUG00000006481	2 retrocopies	retro_mluc_1217, retro_mluc_1369,
Macaca mulatta	ENSMMUG00000020928	11 retrocopies	retro_mmul_1444, retro_mmul_1544, retro_mmul_2149, retro_mmul_2151, retro_mmul_2225, retro_mmul_2226, retro_mmul_2389 , retro_mmul_690, retro_mmul_696, retro_mmul_697, retro_mmul_752,
Monodelphis domestica	ENSMODG00000000152	2 retrocopies	retro_mdom_1271, retro_mdom_737,
Nomascus leucogenys	ENSNLEG00000001163	4 retrocopies	retro_nleu_1756, retro_nleu_1942, retro_nleu_2022, retro_nleu_669,
Pongo abelii	ENSPPYG00000025875	2 retrocopies	retro_pabe_2248, retro_pabe_510,
Pan troglodytes	ENSPTRG00000012419	5 retrocopies	retro_ptro_1072, retro_ptro_1077, retro_ptro_1080, retro_ptro_1378, retro_ptro_415,
Pteropus vampyrus	ENSPVAG00000016707	1 retrocopy	retro_pvam_134,
Sorex araneus	ENSSARG00000006252	1 retrocopy	retro_sara_362,
Tupaia belangeri	ENSTBEG00000001123	4 retrocopies	retro_tbel_1731, retro_tbel_3479, retro_tbel_4589, retro_tbel_926,
Vicugna pacos	ENSVPAG00000005847	2 retrocopies	retro_vpac_136, retro_vpac_265,