RetrogeneDB ID: retro_mmul_2607

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:84898662..84900298(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STIP1
• Ensembl ID: ENSMMUG00000012953
• Aliases: None
• Description: None

Sequence

>retro_mmul_2607
TGTGCTATGAAGCAGGTCAACGAGCTGAAAGAGAACGGCAACAAGGCCCTGAGCACGGCAACATAGATGATGCCTTACAG
TGCTACTCAGAAGCCATTAAGCTGGATCCCCACAACCACATGCTCTACAGCAACTGTTCTTCCCCCTATGCCAAGAAAGG
AGACTACCAGAAGGCTTACAAGGATGGCTGTAAGACCATGGACCTAAAAGCCTGACTGGGGCAACGGCTATTCACAAAAA
GCAGCAGCTCTAGAGTTCTTAAACCGATTTGAAGAAGACAAGAGAACCTACGAGGAGCACTTAAAACAGAGGCAAATAAC
TCTCAACTGAAAGAGGGTTTACAGAATATGGAGGCCAAGTTGGCAGAGAGAAAATTCATGAATGCTTTCAACATGCCCAA
TCTGTATCAGAAGTTGGAGAGTGATCCCAGGACAAGAACACTGCTCAGTGATTCTAACTATCAGGAGCTGATAGAGCAGC
TACAAAACAAGCCTTCTGATCTGGGCAGCAAACTACAAGATCCCCGGATCATGACCACTCTCAGTGTCCTCCTTGAGGTC
GATCTGGGCAGTACGGATGAGGAGGAACAGGTTGCAACACCTCCCACCCCCCACCCCCTCCCAAAAAGGAGACCAAGCCA
GAGCCAGAGGAAGAAGATCTTCCAGAGAAGAAGAAGCAGGCACTGAAAGAAAAAGAGCTGAAGAACAATGCCTACCAGAA
GAAATACTGACCCAGCCTTGAAGCATTACGACAAAGCCAAGGAGCTGGACCCCAGCAATATGACTTACATTACCAATTAA
GCAGTGGTATACTTTGAAAAGGGCGACTACAGTAAGTGCAGGGAGCCTTGTGGGAAGTCCATTTAAGTGGGAGAGAAAAC
AGAAAACCATCTACGGATTGCCAAAGCCTATGCTCGAATTGGCAACTCCTACTTCAAAGAAGAAAGGTACAAGGATGCCA
TCCATTTCTATAACAAGTCTCTTGCAGAGCACCAAACTCCAGATGTGCTCAAGAAATGCCAGCAGGCAGAGAAAATCCTG
AAGGAGCAAGAACGGCTGGCCTGCATAAACCTGGACCAGGCTTTGGAGGAGAAGAACAAAAGAAACTAGTGTTTTCAGAA
AGGGGACTATCCCCAGGACCTGAAGCGTTATACAGAAACCATCAAAAGGAACCCGAAAGATGCCAGATTATACAGCAATC
GAGCTGCCTGGAGTTCCGCCAAACTCCTGGAGTTCCAGCTGGCACTCAAGGACTGTGAGGAATGTATCCAGCTGGAGCCA
AGGGTTCATCAAGGGTTATACACGGAAAGCCGCTGCCCTGGAAGCGATGAAGGACTACACCAAAGCGATGGATGTGTACC
GGAAGGTGCTAGACCTGGACTCGAGCTGTAAGGAGGCGGCAGACGGCTACCAGCGCTGTATGATGGTGCACTACTACCGA
CAACACAGCCCGGAAGAGGTGAGGCGAGGAACAAAAAAAAGACCCCAAGGTGCAGCAGATCATGAGTGACATAGCCATGC
GCCTTATCCTGGAACAGATGCAGAAGGACCCCCAGGCACTCAGCGAACACTTAAAGAATCTTGCAATCGCACAGAAGATC
CAGAAGCTGATGGATGTGGGTTTGATTGCAATTCGG

Alignment

ORF - retro_mmul_2607 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.59 %
• Parental protein coverage: 92.37 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  CSLRWVNELKEKGNKALSA-GNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDL
          C....VNELKE.GNKALS..GNIDDALQCYSEAIKLDPHNH.LYSN.S..YAKKGDYQKAY.DGCKT.DL
Retrocopy CAMKQVNELKENGNKALST<GNIDDALQCYSEAIKLDPHNHMLYSNCSSPYAKKGDYQKAYKDGCKTMDL

Parental  K-PDWGKGYSRKAAALEFLNRFEEAKRTYEEGLKH-EANNPQLKEGLQNMEARLAERKFMNPFNMPNLYQ
          K.PDWG.GYS.KAAALEFLNRFEE.KRTYEE.LK..EANN.QLKEGLQNMEA.LAERKFMN.FNMPNLYQ
Retrocopy K>PDWGNGYSQKAAALEFLNRFEEDKRTYEEHLKQ<EANNSQLKEGLQNMEAKLAERKFMNAFNMPNLYQ

Parental  KLESDPRTRTLLSDPTYRELIEQLRNKPSDLGTLLSWKSIVTPHRNNVGGEAVIQDPVTQRATPPPPPPP
          KLESDPRTRTLLSD..Y.ELIEQL.NKPSDLG..L....I.T.............D...Q.ATPP.P.P.
Retrocopy KLESDPRTRTLLSDSNYQELIEQLQNKPSDLGSKLQDPRIMTTLSVLLEVDLGSTDEEEQVATPPTPHPL

Parental  KKETKPEPMEEDLPENKKQALKEKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDY
          .K.....................K............D.ALKHYDKAKELDP.NMTYITN.A.VYFEKGDY
Retrocopy PKRRPSQSQRKKIFQRRRSRH*KKKS*RTMPTRRNTDPALKHYDKAKELDPSNMTYITN*AVVYFEKGDY

Parental  NKCRELCEKAIDVGRENREDYRQIAKAYARIGNSYFKEEKYKDAIHFYNKSLAEHRTPDVLKKCQQAEKI
          .KCRE.C.K.I.VG.E..E....IAKAYARIGNSYFKEE.YKDAIHFYNKSLAEH.TPDVLKKCQQAEKI
Retrocopy SKCREPCGKSI*VG-EKTENHLRIAKAYARIGNSYFKEERYKDAIHFYNKSLAEHQTPDVLKKCQQAEKI

Parental  LKEQERLAYINPDLALEEKNKGNECFQKGDYPQAMKHYTEAIKRNPKDAKLYSNRAA-CYTKLLEFQLAL
          LKEQERLA.IN.D.ALEEKNK.N.CFQKGDYPQ..K.YTE.IKRNPKDA.LYSNRAA....KLLEFQLAL
Retrocopy LKEQERLACINLDQALEEKNKRN*CFQKGDYPQDLKRYTETIKRNPKDARLYSNRAAWSSAKLLEFQLAL

Parental  KDCEECIQLEPT-FIKGYTRKAAALEAMKDYTKAMDVYQKALDLDSSCKEAADGYQRCMMAQYNRHDSPE
          KDCEECIQLEP..FIKGYTRKAAALEAMKDYTKAMDVY.K.LDLDSSCKEAADGYQRCMM..Y.R..SPE
Retrocopy KDCEECIQLEPR>FIKGYTRKAAALEAMKDYTKAMDVYRKVLDLDSSCKEAADGYQRCMMVHYYRQHSPE

Parental  DVKR-RAMADPEVQQIMSDPAMRLILEQMQKDPQALSEHLKNPVIAQKIQKLMDVGLIAIR
          .V.R.....DP.VQQIMSD.AMRLILEQMQKDPQALSEHLKN..IAQKIQKLMDVGLIAIR
Retrocopy EVRR>EXXXDPKVQQIMSDIAMRLILEQMQKDPQALSEHLKNLAIAQKIQKLMDVGLIAIR

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	3.25 RPM	104.54 RPM
SRP007412_brain_prefrontal_cortex	2.86 RPM	159.06 RPM
SRP007412_cerebellum	3.62 RPM	119.33 RPM
SRP007412_heart	1.53 RPM	86.21 RPM
SRP007412_kidney	1.88 RPM	64.67 RPM
SRP007412_liver	1.46 RPM	50.35 RPM
SRP007412_testis	5.80 RPM	451.53 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2607 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2607 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2607 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015663	2 retrocopies	retro_btau_836, retro_btau_913,
Canis familiaris	ENSCAFG00000014672	6 retrocopies	retro_cfam_1077, retro_cfam_1172, retro_cfam_1722, retro_cfam_1982, retro_cfam_474, retro_cfam_497,
Callithrix jacchus	ENSCJAG00000018209	2 retrocopies	retro_cjac_1043, retro_cjac_2222,
Cavia porcellus	ENSCPOG00000002914	1 retrocopy	retro_cpor_1443,
Felis catus	ENSFCAG00000005937	1 retrocopy	retro_fcat_1510,
Homo sapiens	ENSG00000168439	1 retrocopy	retro_hsap_4867,
Gorilla gorilla	ENSGGOG00000012132	1 retrocopy	retro_ggor_3040,
Microcebus murinus	ENSMICG00000016933	1 retrocopy	retro_mmur_1045,
Macaca mulatta	ENSMMUG00000012953	1 retrocopy	retro_mmul_2607 ,
Nomascus leucogenys	ENSNLEG00000004777	1 retrocopy	retro_nleu_2000,
Pan troglodytes	ENSPTRG00000003820	1 retrocopy	retro_ptro_3242,
Rattus norvegicus	ENSRNOG00000021164	2 retrocopies	retro_rnor_2862, retro_rnor_468,
Ictidomys tridecemlineatus	ENSSTOG00000014262	1 retrocopy	retro_itri_1578,
Tursiops truncatus	ENSTTRG00000010235	1 retrocopy	retro_ttru_1900,