RetrogeneDB ID: retro_cjac_2222

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:28801257..28802829(-)
• 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_2222
GGCCTTGTTGATGATGCCTTACAGAGCTACTCCGAAGCCATTAAGCTGGATCCCCACAACCACTTTCTCTACAGCAACCG
TTCTGCCGCCTGTGCCAAGAAAGGAGACTACTGAAAGGCTTATGAGGACGGCTGCAAGACCGTCGACCTAAAGCCTGACT
GGGGCAAGGGCTAGTCACGAAAAGCAGCAGTTCTTGAGTTCTTAAACCAGTTTGAAGAAGTCAAGCGAACCTACGAAGAG
GGCTAAAACACGAGGTAAATAACCCTCAGCTGAAAGAGGGTTTACAGAATATGGAGGCCAGGTTGGCACAGAGATTATTC
ACGAACGCTTTCAACATGCCCAATCTGTGTCAGAAGTTGGAGAGTGATCCCAGGACAAGGACACTTCTTAGTGATCCCAC
CTACGAGGAGCTGGTAGAGCAGCTGCGAAACAAGCCTTCCGATCTGGGCACGAAACTACAGGATCCCCGGATCATGACCA
CTCTCAGTGTCCTCCTTGGGGTCGATCTGGGCAGTATGGATGAGGAGGAAGAGGTTGCAACACCACCACCACCCCTCCCA
AAAAGGAGACCAAGCCAGAGCCAATGGAAGAAGATCTTCCAGAGAATAAGAAGCAGGCACTGAAAGAAAAAGAGCTGGGG
AACGATATCTAGAAGAAGAAAGACTTTGGCACAGCCTTGAAGCATTACGACAAAGCCAAGGAGCTGGACCCCACCGACAT
GACTTACATTATCAGTCAAGTAGCGGTATACTTTGAAATGGGCGACTACAATAAATGTCGGGAGCTTTGTGAGAAGGCCA
ATGAAGTGGGGAGAGAAAACCGAGAAGACTATCAACAGATTGCCAAAGCTTATGCTGGAATTGGCAACTCCTACTTCAAA
GAAGGAAAGTACAAGGATGCATCCATTTCTATAACAAGTCTCTGGCAGAGCACCGAACCCCAGATGTGCTCAAGAAATGC
CAGCAGGCAGAGAAAACACTGAAGGAGCAAGAGCAGCTGGCCTACATAAACCCCGACCTGGCTTTGGAGGAGAAGAACAA
AGGCAACGAGTGTTTTCAGAAAGGGGAGTATCCCCAGGCCGTGAAGCATTATACAGAGGACGTCAAAAGGAATCCAAAAG
ATGCCAAATTGTACAGTGATCGAGCTGCCTTCTGCACCAAACTTCTGGAGTTCCAGCTGGCACTCAAGGACTGTGAGGAA
TGTATCCAGCTGGAGCCGACCTTTATCAAGGGTTATACCCGGAAAGCCTCTGCCCTGGGAGCGATGAAGGACTGCACCAA
AGCCATGGGTGTGTACCAGAAGGCGCTCGACCGGGACTCCAGCTGTAAGGAGGCGGCAGCCGGCTACCAGCGCTGTATGA
TGGCGTAATGCAACCGGCTTGACAGTCCGGAAGATGTGAAACGACCAGCCATGGCCGACCCCGAGGTGCAGCACATTATG
AGTGACCCAGCCATGCGCCTTATCCTGGAACAGATGCAGAAGGACCCCCAGGCACTCAGCGAACACTTAGAGAATCCTGT
AATAGCACAGAAGATCCAGAAGCTGATGGATGTCGGTCTGATTGCAATTCGG

Alignment

ORF - retro_cjac_2222 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.41 %
• Parental protein coverage: 96.87 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GNIDDALQCYSEAIKLDPHNHLLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALEFLNR
          G..DDALQ.YSEAIKLDPHNH.LYSNRSAA.AKKGDY.KAYEDGCKTVDLKPDWGKG.SRKAA.LEFLN.
Retrocopy GLVDDALQSYSEAIKLDPHNHFLYSNRSAACAKKGDY*KAYEDGCKTVDLKPDWGKG*SRKAAVLEFLNQ

Parental  FEEAKRTYEEG-LKHEANNPQLKEGLQNMEARLAERKFMNPFNMPNLYQKLENDPRTRTLLSDPTYRELV
          FEE.KRTYEEG.LKHE.NNPQLKEGLQNMEARLA.R.F.N.FNMPNL.QKLE.DPRTRTLLSDPTY.ELV
Retrocopy FEEVKRTYEEG<LKHEVNNPQLKEGLQNMEARLAQRLFTNAFNMPNLCQKLESDPRTRTLLSDPTYEELV

Parental  EQLRNKPSDLGTKLQDPRIMTTLSVLLGVDLGSMDEEEEVATPPPPP-PPKKETKPEPMEEDLPENKKQA
          EQLRNKPSDLGTKLQDPRIMTTLSVLLGVDLGSMDEEEEVATPP.PP.PPKKETKPEPMEEDLPENKKQA
Retrocopy EQLRNKPSDLGTKLQDPRIMTTLSVLLGVDLGSMDEEEEVATPP-PP<PPKKETKPEPMEEDLPENKKQA

Parental  LKEKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYDKCRELCEKAIEVGRENRED
          LKEKELGND..KKKDF.TALKHYDKAKELDPT.MTYI..Q.AVYFE.GDY.KCRELCEKA.EVGRENRED
Retrocopy LKEKELGNDI*KKKDFGTALKHYDKAKELDPTDMTYIISQVAVYFEMGDYNKCRELCEKANEVGRENRED

Parental  YRQIAKAYARIGNSYFKEEKYKDA-IHFYNKSLAEHRTPDVLKKCQQAEKILKEQERLAYINPDLALEEK
          Y.QIAKAYA.IGNSYFKE.KYKDA.IHFYNKSLAEHRTPDVLKKCQQAEK.LKEQE.LAYINPDLALEEK
Retrocopy YQQIAKAYAGIGNSYFKEGKYKDA<IHFYNKSLAEHRTPDVLKKCQQAEKTLKEQEQLAYINPDLALEEK

Parental  NKGNECFQKGDYPQAMKHYTEAIKRNPKDAKLYSNRAACYTKLLEFQLALKDCEECIQLEPTFIKGYTRK
          NKGNECFQKG.YPQA.KHYTE..KRNPKDAKLYS.RAA..TKLLEFQLALKDCEECIQLEPTFIKGYTRK
Retrocopy NKGNECFQKGEYPQAVKHYTEDVKRNPKDAKLYSDRAAFCTKLLEFQLALKDCEECIQLEPTFIKGYTRK

Parental  AAALEAMKDYTKAMDVYQKALDLDSSCKEAADGYQRCMMAQYNRHDSPEDVKRRAMADPEVQQIMSDPAM
          A.AL.AMKD.TKAM.VYQKALD.DSSCKEAA.GYQRCMMA..NR.DSPEDVKR.AMADPEVQ.IMSDPAM
Retrocopy ASALGAMKDCTKAMGVYQKALDRDSSCKEAAAGYQRCMMA*CNRLDSPEDVKRPAMADPEVQHIMSDPAM

Parental  RLILEQMQKDPQALSEHLKNPVIAQKIQKLMDVGLIAIR
          RLILEQMQKDPQALSEHL.NPVIAQKIQKLMDVGLIAIR
Retrocopy RLILEQMQKDPQALSEHLENPVIAQKIQKLMDVGLIAIR

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	0.02 RPM	40.11 RPM
SRP051959_heart	0.00 RPM	43.62 RPM
SRP051959_kidney	0.02 RPM	48.83 RPM
SRP051959_liver	0.04 RPM	46.96 RPM
SRP051959_lung	0.08 RPM	62.66 RPM
SRP051959_lymph_node	0.11 RPM	77.60 RPM
SRP051959_skeletal_muscle	0.07 RPM	58.05 RPM
SRP051959_spleen	0.02 RPM	59.10 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2222 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2222 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2222 has 0 orthologous retrocopies within eutheria group .

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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,