RetrogeneDB ID: retro_cjac_899

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:32650158..32651966(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000008172
• Aliases: None
• Description: None

Sequence

>retro_cjac_899
CGCATTGTGTCTTGGTGGATGACGGGACGGAGCCCAGCAGCTGAAGACACCCGCTGGGTCATGTGGTTCGGAGACGACAA
GTTTTCAGTGGTGTGTGTTGAGAAGCTGATGCCGCTGAGCTCATTTTGCAGTGCGTTCCACCAGGCCACGTACAACAAGC
AGCCCATGTACAGCAAAGCCATCTTTGAGGTCCTGCAGGTGGCCACCAGCCATGAGGAGAAGCTGTTCCCAGTGTGCCAC
GACAGCAACAAGAGTGACACTACCAAGGCCATGGAGGTGCAGAACAAGCAGATGACTGAATGGGCTCTGGGAGCTTCCAG
CCCTCTGGTCCCAAGGGCCTGGAGCCACCAGAAGAGGAAAAGAAGCCCTACAGAGAAGTGTATATGCACATGTGGGTGGA
ACCTGAGGCAGCTGCCTACGCACCACCTCCACCAACCAAAAAGCCCTGGGAGAGCACAACGGAGAAGCCCAAGGTCAGAG
AGATCATCGATGAGCACACAAGAGAGCGGCTGGTGTACGAGGTGTGGCAGAAGTTCTGGAACATCGAGGACATCTGCATC
TCCTGTGGGAGCCTCAACATCACCCTGAAACACCCCCTCTTCATTGGAGGAATGTGTCAAAACTGCAAGAACTGCTTTCT
GGAGTGTGCATACTGGTACAACGATGATGGCTATCAGTCCTACTGCACCATCTGCTGTGGGGGCCGAGAGGTGCTCATGT
GCGGGAACAACTGCTGCAGGTGCTTTTGTGGGGAATGTGTGGACCTCTTGGTGGGGCTGGGGGCTGCCCAGGCAGCCATT
AAGGAAGACCCCTGGAACTGCTACATGTGTGGGCACAAGGGCACCTACGGGCTGCTGCAGCAGTGAGACGACTGGCCCTC
CCAGCTCCAGATGTTCTTTGCCAATAACCACGACCAGGTATTTAACCCTCCAAAGGTTTACCCACCTGTCCCAGCTGAGA
AGAGGAAGCCCATCTCAGTGCTGTCTCTCTTTGATGGAATTGCTACAGGGCTTCTGGTGCTGAAGGACTTGGGCATTCAG
GTGGACCGCTACATTGCCTCTGAGGTGTGTGAGGGCTCCATCACAATGGGCATGGTGCGGCACCAGGGGAAGATCATGTA
CGTCGGGGATGTCCGCAGCGTCACACAGAAGCATATCCAGGAGTGGGGCCCATTCGATCTTGTGATTGGGGGCAGTCCCT
GCAATGACCTCTCCATTGTCAACCCTGTTCGCCAGGGCCTCTATGAGGACACTGGCCTGCTCTTCTTTGAGTTCTACCAC
CTATTGCGTGGCATGCGGCCCAAGGAGGGAGATGATCGCCCCTTCTTCTGGCTCTTTGAGAATGTGGTGGCCATGGGCGT
TAGTGACAAGAGGGACATATTGCGATTTCTTGAGTCCATCCCTGTGATGATTGATTCCAAAGAAGTGTCAGCTGCACACA
GGGCCCGCTACTTCTGGGGTAACCTTCCCGGTATGAACAGGCTGTTGACATCCACTGTGAATGATAAGCTGGAGCTGCAG
GAGTGTCTGGAGCATGGAAGGATAGCCAAGTTCAGCAAACTGAGGACCATTACTACAAGGTCAAACTCCATAAAGCAAGG
CAAATACCAGCAATTCACCGTCTTCATGAATGAGGAAGAGGACATCCTATGGTGCACTGAAATGGAAAGGGTATTTAATT
TGCCTGTCCACTATACTGAAGTCTCCAACATGAGCCACTTGGTGAGGCAGCGACTGCTGGGCCGGTCGTGGAGTGTGCCA
GTCAACCGCCACCTCTTCACTCCGTTGAAGGAGTATTTTGCGTGTGTG

Alignment

ORF - retro_cjac_899 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.6 %
• Parental protein coverage: 66.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RIVSWWMTGRSRAAEGTRWVMWFGDGKFSVVCVEKLMPLSSFCSAFHQATYNKQPMYRKAIYEVLQVASS
          RIVSWWMTGRS.AAE.TRWVMWFGD.KFSVVCVEKLMPLSSFCSAFHQATYNKQPMY.KAI.EVLQVA.S
Retrocopy RIVSWWMTGRSPAAEDTRWVMWFGDDKFSVVCVEKLMPLSSFCSAFHQATYNKQPMYSKAIFEVLQVATS

Parental  RAGKLFPVCHDSDESDTAKAVEVQNKQMIEWALGG-FQPSGPKGLEPPEEEKNPYKEVYTDMWVEPEAAA
          ...KLFPVCHDS..SDT.KA.EVQNKQM.EWALG..FQPSGPKGLEPPEEEK.PY.EVY..MWVEPEAAA
Retrocopy HEEKLFPVCHDSNKSDTTKAMEVQNKQMTEWALGA<FQPSGPKGLEPPEEEKKPYREVYMHMWVEPEAAA

Parental  YAPPPPAKKPRKSTTEKPKVKEIIDERTRERLVYEVRQKCRNIEDICISCGSLNVTLEHPLFIGGMCQNC
          YAPPPP.KKP..STTEKPKV.EIIDE.TRERLVYEV.QK..NIEDICISCGSLN.TL.HPLFIGGMCQNC
Retrocopy YAPPPPTKKPWESTTEKPKVREIIDEHTRERLVYEVWQKFWNIEDICISCGSLNITLKHPLFIGGMCQNC

Parental  KNCFLECAYQYDDDGYQSYCTICCGGREVLMCGNNNCCRCFCVECVDLLVGPGAAQAAIKEDPWNCYMCG
          KNCFLECAY.Y.DDGYQSYCTICCGGREVLMCGNN.CCRCFC.ECVDLLVG.GAAQAAIKEDPWNCYMCG
Retrocopy KNCFLECAYWYNDDGYQSYCTICCGGREVLMCGNN-CCRCFCGECVDLLVGLGAAQAAIKEDPWNCYMCG

Parental  HKGTYGLLRRRDDWPSRLQMFFANNHDQEFDPPKVYPPVPAEKRKPIRVLSLFDGIATGLLVLKDLGIQV
          HKGTYGLL...DDWPS.LQMFFANNHDQ.F.PPKVYPPVPAEKRKPI.VLSLFDGIATGLLVLKDLGIQV
Retrocopy HKGTYGLLQQ*DDWPSQLQMFFANNHDQVFNPPKVYPPVPAEKRKPISVLSLFDGIATGLLVLKDLGIQV

Parental  DRYIASEVCEDSITVGMVRHQGKIMYVGDVRSVTQKHIQEWGPFDLVIGGSPCNDLSIVNPARKGLYEGT
          DRYIASEVCE.SIT.GMVRHQGKIMYVGDVRSVTQKHIQEWGPFDLVIGGSPCNDLSIVNP.R.GLYE.T
Retrocopy DRYIASEVCEGSITMGMVRHQGKIMYVGDVRSVTQKHIQEWGPFDLVIGGSPCNDLSIVNPVRQGLYEDT

Parental  GRLFFEFYRLLHDARPKEGDDRPFFWLFENVVAMGVSDKRDISRFLESNPVMIDAKEVSAAHRARYFWGN
          G.LFFEFY.LL...RPKEGDDRPFFWLFENVVAMGVSDKRDI.RFLES.PVMID.KEVSAAHRARYFWGN
Retrocopy GLLFFEFYHLLRGMRPKEGDDRPFFWLFENVVAMGVSDKRDILRFLESIPVMIDSKEVSAAHRARYFWGN

Parental  LPGMNRPLASTVNDKLELQECLEHGRIAKFSKVRTITTRSNSIKQGKDQHFPVFMNEKEDILWCTEMERV
          LPGMNR.L.STVNDKLELQECLEHGRIAKFSK.RTITTRSNSIKQGK.Q.F.VFMNE.EDILWCTEMERV
Retrocopy LPGMNRLLTSTVNDKLELQECLEHGRIAKFSKLRTITTRSNSIKQGKYQQFTVFMNEEEDILWCTEMERV

Parental  FGFPVHYTDVSNMSRLARQRLLGRSWSVPVIRHLFAPLKEYFACV
          F..PVHYT.VSNMS.L.RQRLLGRSWSVPV.RHLF.PLKEYFACV
Retrocopy FNLPVHYTEVSNMSHLVRQRLLGRSWSVPVNRHLFTPLKEYFACV

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	10.61 RPM
SRP051959_heart	0.00 RPM	17.58 RPM
SRP051959_kidney	0.07 RPM	21.88 RPM
SRP051959_liver	0.00 RPM	10.87 RPM
SRP051959_lung	0.02 RPM	16.79 RPM
SRP051959_lymph_node	0.00 RPM	21.51 RPM
SRP051959_skeletal_muscle	0.00 RPM	20.03 RPM
SRP051959_spleen	0.02 RPM	24.77 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_899 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_899 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_899 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008172	2 retrocopies	retro_cjac_4163, retro_cjac_899 ,
Microcebus murinus	ENSMICG00000004108	2 retrocopies	retro_mmur_1086, retro_mmur_797,
Monodelphis domestica	ENSMODG00000015850	1 retrocopy	retro_mdom_859,
Oryctolagus cuniculus	ENSOCUG00000024688	1 retrocopy	retro_ocun_564,