RetrogeneDB ID: retro_cjac_1043

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:65005949..65007375(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STIP1
• Ensembl ID: ENSCJAG00000018209
• Aliases: None
• Description: None

Sequence

>retro_cjac_1043
GACCATCAACCTGACTGGGGCAAGAGCTATTCACAAAAAGCCGCAGCTCTTGAGTTCTTAAACGAATTTGAAGAAGCCAA
GCAAACCTATGAGGAGGGCTTAAAACACGAAGCAAATAACTCTCATATAAAAGAGGGTTTACAGAATATGCAGGCCAGAT
TGGCAGAGAGAAAATCCGTGAACCCTTTCAACATGCCCAATCTGTATCAGAAGTTGGAGAGTGATCCCAGGACAAGGACA
CTACTCAGTGATCCTACCTACCTGGAGCTGATAGAGCAGCTGTGAAACAAGCCTTCCAATCTGGGCACAAAACTACCAGA
TCCCTGGCTTATGACCACTCTCAGTGTCCTCCTGAGGGTCAACCTTGGCTGTATAAGTGAGGAAGAAGTTGCAACACCTC
CACCACAATATCCTCCCAAAAAGGAGACCAACTCAGAGCTAATGGGAGAAGATATTCCAGAGAATAGGAAACAGGTGCTG
AAATAAAAAGCTGGGAACAATGCCTACAAGAAGAAAGACTTTGACACAACCCTGAAGCGTTTTGACAAAGCCAAGGAGCT
AGACCCCATCATGACTTACATTACCAATCAAGCAGCAGTATACTTTGAAAAGGGTGACTACAATAAGTGCTGGGAGCTTT
GTAAGAAAGCCATTGAAGTAGGGAGAGAAAACCAAGAAGACTGTGGACAGATCACCAGACCTTATGCTCAAATTGGCAAC
TCCTACTTCAAAGAAGAAAAGTACAAGGATGCCATCCATTTCTATAACAGGTATCTGGCAGAGCACCTGATCCTAGATGT
GCTCAAGAAATGCCAGTAGGCAGAGAAAATCCTGAAAAAGCAAGGGCAGCTGGCATACATAAACCCCAACTTGGCTTTGG
AGGAGAAGAACAAAGGCAATGAGTGTTTTCAGAAAGGGGATTATCCCCAGGCCACGAAGCATTATGCAGAAGCCATCAAA
AGGAACCCAAAAGATGCTAAATTATACAACAGTCAAGCTGCCTGCTACACCAGACTCCTGGAGTTCCAGATGACACTCAA
GGACTGTGAAGAATATATCCAGCTGGAGCTGACCTTCATCAAGGGTTACACATGGAAAGCAGCAGCCCTGGAAGTGTTGA
AGGACTACACCAAAGCCATAGTTGTGTACCAGAAGGCACTAGACCTAGACTTCAGCTGTAAGGAGGTGGCAACCGGCTAA
CAGCACTGTATGATGGCACAGTACAACCAGCATGACAGTCCAGAAGATGTGAAGTGAGGAGCCATGGCTGACCCAGAGGT
GCAGCAGATCATGAGAGACCCAGCCAATGCACCTTATCCTGGAACAGATGCAGAAGCATCCCCAGACACTCAGCAAACAT
TCAAAGAATCTTGTAGTAGCACGGAAGATCCAGAAGCTAATGGATGTGGGTCTGATTGCAATTCAG

Alignment

ORF - retro_cjac_1043 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.54 %
• Parental protein coverage: 88.03 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DLKPDWGKGYSRKAAALEFLNRFEEAKRTYEEGLKHEANNPQLKEGLQNMEARLAERKFMNPFNMPNLYQ
          D..PDWGK.YS.KAAALEFLN.FEEAK.TYEEGLKHEANN...KEGLQNM.ARLAERK..NPFNMPNLYQ
Retrocopy DHQPDWGKSYSQKAAALEFLNEFEEAKQTYEEGLKHEANNSHIKEGLQNMQARLAERKSVNPFNMPNLYQ

Parental  KLENDPRTRTLLSDPTYRELVEQLRNKPSDLGTKLQDPRIMTTLSVLLGVDLGSMDEEEEVATPPPPPPP
          KLE.DPRTRTLLSDPTY.EL.EQL.NKPS.LGTKL.DP..MTTLSVLL.V.LG...EEE.VATPPP..PP
Retrocopy KLESDPRTRTLLSDPTYLELIEQL*NKPSNLGTKLPDPWLMTTLSVLLRVNLGCISEEE-VATPPPQYPP

Parental  KKETKPEPMEEDLPENKKQALKEKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDY
          KKET..E.M.ED.PEN.KQ.LK.K..GN.AYKKKDFDT.LK..DKAKELDP..MTYITNQAAVYFEKGDY
Retrocopy KKETNSELMGEDIPENRKQVLK*KA-GNNAYKKKDFDTTLKRFDKAKELDPI-MTYITNQAAVYFEKGDY

Parental  DKCRELCEKAIEVGRENREDYRQIAKAYARIGNSYFKEEKYKDAIHFYNKSLAEHRTPDVLKKCQQAEKI
          .KC.ELC.KAIEVGREN.ED..QI...YA.IGNSYFKEEKYKDAIHFYN..LAEH...DVLKKCQ.AEKI
Retrocopy NKCWELCKKAIEVGRENQEDCGQITRPYAQIGNSYFKEEKYKDAIHFYNRYLAEHLILDVLKKCQ*AEKI

Parental  LKEQERLAYINPDLALEEKNKGNECFQKGDYPQAMKHYTEAIKRNPKDAKLYSNRAACYTKLLEFQLALK
          LK.Q..LAYINP.LALEEKNKGNECFQKGDYPQA.KHY.EAIKRNPKDAKLY...AACYT.LLEFQ..LK
Retrocopy LKKQGQLAYINPNLALEEKNKGNECFQKGDYPQATKHYAEAIKRNPKDAKLYNSQAACYTRLLEFQMTLK

Parental  DCEECIQLEPTFIKGYTRKAAALEAMKDYTKAMDVYQKALDLDSSCKEAADGYQRCMMAQYNRHDSPEDV
          DCEE.IQLE.TFIKGYT.KAAALE..KDYTKA..VYQKALDLD.SCKE.A.G.Q.CMMAQYN.HDSPEDV
Retrocopy DCEEYIQLELTFIKGYTWKAAALEVLKDYTKAIVVYQKALDLDFSCKEVATG*QHCMMAQYNQHDSPEDV

Parental  KRRAMADPEVQQIMSDPA-MRLILEQMQKDPQALSEHLKNPVIAQKIQKLMDVGLIAIR
          K..AMADPEVQQIM.DPA.M.LILEQMQK.PQ.LS.H.KN.V.A.KIQKLMDVGLIAI.
Retrocopy K*GAMADPEVQQIMRDPA>MHLILEQMQKHPQTLSKHSKNLVVARKIQKLMDVGLIAIQ

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
SRP051959_colon	0.00 RPM	40.11 RPM
SRP051959_heart	0.00 RPM	43.62 RPM
SRP051959_kidney	0.00 RPM	48.83 RPM
SRP051959_liver	0.06 RPM	46.96 RPM
SRP051959_lung	0.02 RPM	62.66 RPM
SRP051959_lymph_node	0.00 RPM	77.60 RPM
SRP051959_skeletal_muscle	0.09 RPM	58.05 RPM
SRP051959_spleen	0.00 RPM	59.10 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1043 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1043 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1043 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,