RetrogeneDB ID: retro_mmul_1802

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:149565636..149566573(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2487
• Ensembl ID: ENSMMUG00000007740
• Aliases: None
• Description: None

Sequence

>retro_mmul_1802
GGCAGTATTGGCTCCCTCACGGACATAGTTGATATGTTATTTGAAGGAAGAGGAAGGATGCAGAAAGAAAAAGAGGTAAA
AATATTGTGCATCAGCTCTCAGTAACCACAGAAGATGTATTTAATGGTGCAACAAGAAAACTAGCTCCATAAAATAATGT
GATTTGTGACAAGTGTGTAGGCCAAGGTGGTAAGAAAGGAGCAGTAGAGTGCTGTCCCAATCACTGAAGTACTAGAATGC
AAATAAGAATCATCAGATAGGACCTAGAATGGCTCAAGAATCTCAGTCTGTGTGCATGGAGTGCCAGAGCCATGGGGAGC
AGAACAGTCCTAATGACAGATGTAAAAGCTGCAATGGAAGGAAGATAGTTTGAGAGAAGAAGAGCCTACAAGTTCACGAC
AAAGGCATGAAAGACGACCAGTAGATATCTTTCATGGTGAAGGAGATCAGGAGCCAGGAGATATTATCATTGTTTTAGAT
CAGAAGGACCATGCTTCCTTATTCGACCAGAAGACCTTTTCATGTGTATGGACATAAAACTGGTTGAAGCGCTGCATGGC
TTCCAAAAGCCAATACCCACCCTTGACAACCAAACCCCAGTCAACACCTCTCATCCCCCAACTCAGATTGTCAAGCATAG
AGATACTAAGTGTGTGCTAAATGAAGGCATGACAGTTTATTGTAGATCCTATGAAAAGGATCACCTAAGCATCAAATTTA
AGGTCTACTTTCCTGAGAATGCCTTTCTGTCTCCTGATAAACATTTTTTGCTGTAATAACTCCTGCCTGAGAGATAGGAA
GTAAAAGAGGCTGATGAAATGGATCAAGTACATCTGGTGGATGTTGACTGGTATCAGCAAGGATGGGCCATTACAATGGA
GAAGCTTATGAGGATGATGAACATCATGCCAGAAGTGGTGTTCAGTGTCAAACCTCT

Alignment

ORF - retro_mmul_1802 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.46 %
• Parental protein coverage: 80.35 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GGFGSPMDIFDMFFGGGGRMQRER-RGKNVVHQLSVTLEDLYNGATRKLALQKNVICDKCEGRGGKKGAV
          G..GS..DI.DM.F.G.GRMQ.E..RGKN.VHQLSVT.ED..NGATRKLA...NVICDKC.G.GGKKGAV
Retrocopy GSIGSLTDIVDMLFEGRGRMQKEK<RGKNIVHQLSVTTEDVFNGATRKLAP*NNVICDKCVGQGGKKGAV

Parental  ECCPNCRGTGMQIRI-HQIGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIVREKKILEVHIDKGM
          ECCPN...T.MQIRI.HQIGP.M.Q..QSVCMECQ.HGE..SP.DRCKSCNGRKIV.EKK.L.VH.DKGM
Retrocopy ECCPNH*STRMQIRI<HQIGPRMAQESQSVCMECQSHGEQNSPNDRCKSCNGRKIV*EKKSLQVH-DKGM

Parental  KDGQKITF-HGEGDQEPGLEPGDIIIVL-DQKDHAVFTRRGEDLFMCMDIQLVEALCGFQKPISTLDNRT
          KD.Q.I.F.HGEGDQ....EPGD.II..........F..R.EDLFMCMDI.LVEAL.GFQKPI.TLDN.T
Retrocopy KDDQ*ISF<HGEGDQ----EPGD-IIIV<FRSEGPCFLIRPEDLFMCMDIKLVEALHGFQKPIPTLDNQT

Parental  IVITSHPG-QIVKHGDIKCVLNEGMPIYRRPYEKGRLIIEFKVNFPENGFLSPDKLSLLEKLLPERKEVE
          .V.TSHP..QIVKH.D.KCVLNEGM..Y.R.YEK..L.I.FKV.FPEN.FLSPDK..LL..LLPER.EV.
Retrocopy PVNTSHPPTQIVKHRDTKCVLNEGMTVYCRSYEKDHLSIKFKVYFPENAFLSPDKHFLL**LLPER*EVK

Parental  ETDEMDQVELVDFDPNQE-RRRHYNGEAYEDDEHHPRGGVQCQTS
          E.DEMDQV.LVD.D..Q..R..HYNGEAYEDDEHH.R.GVQCQTS
Retrocopy EADEMDQVHLVDVDWYQQ<RMGHYNGEAYEDDEHHARSGVQCQTS

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	212.00 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	192.85 RPM
SRP007412_cerebellum	0.00 RPM	107.58 RPM
SRP007412_heart	0.00 RPM	79.67 RPM
SRP007412_kidney	0.00 RPM	94.25 RPM
SRP007412_liver	0.00 RPM	82.02 RPM
SRP007412_testis	0.15 RPM	424.47 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1802 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1802 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1802 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3647
Pan troglodytes	retro_ptro_2472
Gorilla gorilla	retro_ggor_2463
Pongo abelii	retro_pabe_2994

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 58 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007589	4 retrocopies	retro_amel_1509, retro_amel_455, retro_amel_756, retro_amel_946,
Canis familiaris	ENSCAFG00000001818	23 retrocopies	retro_cfam_1111, retro_cfam_1153, retro_cfam_1218, retro_cfam_1229, retro_cfam_1315, retro_cfam_1352, retro_cfam_1420, retro_cfam_1457, retro_cfam_1520, retro_cfam_1668, retro_cfam_1833, retro_cfam_1941, retro_cfam_1949, retro_cfam_1994, retro_cfam_2004, retro_cfam_2162, retro_cfam_352, retro_cfam_391, retro_cfam_419, retro_cfam_749, retro_cfam_751, retro_cfam_923, retro_cfam_993,
Felis catus	ENSFCAG00000008729	5 retrocopies	retro_fcat_1241, retro_fcat_1407, retro_fcat_1502, retro_fcat_1984, retro_fcat_811,
Gorilla gorilla	ENSGGOG00000007030	3 retrocopies	retro_ggor_1603, retro_ggor_2463, retro_ggor_418,
Macaca mulatta	ENSMMUG00000002247	1 retrocopy	retro_mmul_36,
Macaca mulatta	ENSMMUG00000007740	6 retrocopies	retro_mmul_1313, retro_mmul_1802 , retro_mmul_2477, retro_mmul_2482, retro_mmul_2625, retro_mmul_400,
Monodelphis domestica	ENSMODG00000003384	7 retrocopies	retro_mdom_1140, retro_mdom_1253, retro_mdom_1451, retro_mdom_1627, retro_mdom_1824, retro_mdom_742, retro_mdom_874,
Nomascus leucogenys	ENSNLEG00000005268	4 retrocopies	retro_nleu_1255, retro_nleu_2550, retro_nleu_2793, retro_nleu_509,
Oryctolagus cuniculus	ENSOCUG00000004833	2 retrocopies	retro_ocun_516, retro_ocun_70,
Sarcophilus harrisii	ENSSHAG00000012366	1 retrocopy	retro_shar_762,
Sus scrofa	ENSSSCG00000011000	2 retrocopies	retro_sscr_134, retro_sscr_984,