RetrogeneDB ID: retro_cjac_1850

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:144501210..144503614(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000014853
• Aliases: None
• Description: None

Sequence

>retro_cjac_1850
GTTCGGAAAACAGCAGCAGTCTGTGTGGCAAAACTCCATGATCAGGGATTTCTGGATTTTCTATGGGATCTCATAGCAAA
TGCAAATTCAATGGTGGTTGCTAATGCTGTAGCAGCATTATCTGAAATCAGTGAGTCTCACCCAAATAGCAACTTACTCG
ATCTGAACCCACAGAACAATAAGCTGCTAACAGCCCTCAATGAGTGCACTGAATGGGTCCAGATTTTCATCTTCGACTGC
CTGTCTAATTATAACCCTAAAGATGATCGGGAGGCTCAGAGTATCTGTGAATGGGTAACTCCCTGGCTATCCCATGCCAA
CTCAGCAGTGGTGCTTTCAGCGGTAAAAGTCCTAATGAAGTTTCTAGAATTGTTACCTAAGGATTCTGACTACTACAATA
TGCTGCTGAAGAAGTTAGCCCCTCCACTTGTCACTTTGCTTTCTGAGGAGCCAGAAGTGCAGTACATTGCCCTAAGGAAC
ATCAACTTAATATGTTCAGAAAAGGCCTGAAATCTTGAAGCAGGAAATCAAAGTCTTCTTTGTGAAGTACAATGATCCCA
TCTATGTTAAATGAGAGAAGTTGGACATCATGATTCATTTGGCATCTCAAGCCAACATTGCTCAGGTTCTGGCAGAACTG
AAGGAATATGCCACAGAGGTAGATGTTGACTTTGTTCGAAAAGCTGTGCGGGCCATTGGATGGTGTGCCATCAAGGTGAA
GCAATCTGCAGAGCGCTGTGTAAGCACATTGCTTGATCTAATCCAGACCAAAGTGAATTATGTAGTCCAAGAAGCAATTG
TTGTCATCAGGGACATCTTCCGCAAATACCCCAACAAGTATGAAAGTATCATTGCCGCTCTATGTGAGAACTTAGACCCA
CTAGATGAGCCAGATGCTTGAGCAGCTATGATTTGGATTGTGGGAGAATATGCTGAAAGAATTGACAATGCAGATGAGTT
ACTAGAAAGCTTCCTGGAGGGTTTTCACGATGAAAGCACCCAAGTGCAGCTCACTCTGCTTACTGCCATAGTGAAGCTGT
TTCTCAAGAAACCATCAGAAACACAGGAGCTAGTCCAGCAGGTCTTGAGTTTGGCATCACAGGATTCTGATAATCCTGAC
CTTTGAGACTGGGGCTATATTTACTGGTGTCTTCTCTGGACTGACCCTGTCACAGCTAAATAAGTAGTCTTGTCTGAAAA
GCCACTGATCTCTGAGGAGACAGACCTTACTGAGCCAACTCTGCTGGATGAGCTAATTTGCCACATTGGTTCTTTGGCCT
CTGTGTATCATAAGCCTCCCAATGCTTTTGTGGAAGAAAGTCATGTAATCCATCGTAAACACTTGCCAATTCATCATGGG
AGCACTGATGCAGGTGACAGCCCTGTTGGCACCACCATTGCAATGAACCTGGAACAGCCTCAGGTTATCCCCTCTCAAGG
TGATCTTCTAGGGGATCTTTTAAACCTTGACCTTGGTCCCCCAGTCAATGTGCCACAGGTGTCTTCCATGCAGATGGGAG
CAGTGGATCTCCTAGGAGGAGGACTAGATAGTCTGCTTGGCGGGGGCATTGGAGGAAGTCCGGCAGTAGGACAATCCTTT
ATCCCATCATCAGTGCCTGAAACCTTTGCTCCTTCACCTATACCTGCTGTCATCAGCAGTGGACTGAATGACCTGTTTGA
ACTCTCTACAGGGATAGGCATAGCACCCAGTGGATATGTGGCTCCTAAGGCTGTCTGGCTACCTGCAGTAAAAGCTAAAG
GCTTGGAGATTTCAGGAACATTTACTCACCGCCAAGGGCACATCTATATGGAAATGAACTTCACCAATAAAGCTCTGCAG
CATATGACAGATTTTGCAATCCAGTTTAACAAAAATAGCTTTGGTGTCATCCCCAGCACTCCTCTGGCCATCCATACACC
ACTCATGCCAAACCAGAGCATTGATGTCTCCCTGCCTCTCAACACCTTGGGCCCAGTCATGAAGATGGAACCTCTGAATA
ACCTGCAGGTGGCTGTGAAAAACAATACCGATGTCTTCTACTTCAGCTGCCTCATCCCACTCAATGTGCTTTTTGTAGAA
AAAAGCAAAATGGAGCGCCAGGTCTTTCTTGCAACATGGAAGGATATTCCCAATGAAAATGAACTTCATTTTCAGATTAA
GGAATGTCATTTAAATGCTGACACTGTTTCCAGCAAGTTGCAAAACAACAATGTTTATACTATTGCCAAGAGGAATGTGG
AAGGGCAGGATATGCTGTACCAATCCCTGAAGCTCACTAATGGCATTTGGATTTTGGCCGAGCTATGTATCCAGCCAGGA
AACCCCAATTATACACTGTCACTGAAGTGTAGAGCTCCTTAAGTCTCTCAATACATCTCTCAGGTCTACGACAGCATTTT
GAAA

Alignment

ORF - retro_cjac_1850 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.81 %
• Parental protein coverage: 84.75 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANAVAALSEISESHPNSNLLDLNPQNINKLLTALNEC
          V.K..........DQGFLD.L.DLIA..N.MVVANAVAALSEISESHPNSNLLDLNPQN.NKLLTALNEC
Retrocopy VRKTAAVCVAKLHDQGFLDFLWDLIANANSMVVANAVAALSEISESHPNSNLLDLNPQN-NKLLTALNEC

Parental  TEWGQIFILDCLSNYNPKDDREAQSICERVTPRLSHANSAVVLSAVKVLMKFLELLPKDSDYYNMLLKKL
          TEW.QIFI.DCLSNYNPKDDREAQSICE.VTP.LSHANSAVVLSAVKVLMKFLELLPKDSDYYNMLLKKL
Retrocopy TEWVQIFIFDCLSNYNPKDDREAQSICEWVTPWLSHANSAVVLSAVKVLMKFLELLPKDSDYYNMLLKKL

Parental  APPLVTLLSGEPEVQYVALRNINLI-VQKRPEILKQEIKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQ
          APPLVTLLS.EPEVQY.ALRNINLI.VQKRPEILKQEIKVFFVKYNDPIYVK.EKLDIMI.LASQANIAQ
Retrocopy APPLVTLLSEEPEVQYIALRNINLI>VQKRPEILKQEIKVFFVKYNDPIYVK*EKLDIMIHLASQANIAQ

Parental  VLAELKEYATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFRKYPN
          VLAELKEYATEVDVDFVRKAVRAIG.CAIKV.QSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFRKYPN
Retrocopy VLAELKEYATEVDVDFVRKAVRAIGWCAIKVKQSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFRKYPN

Parental  KYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQVQLTLLTAIVKLFL
          KYESIIA.LCENLD.LDEPDA.AAMIWIVGEYAERIDNADELLESFLEGFHDESTQVQLTLLTAIVKLFL
Retrocopy KYESIIAALCENLDPLDEPDA*AAMIWIVGEYAERIDNADELLESFLEGFHDESTQVQLTLLTAIVKLFL

Parental  KKPSETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVTAKEVVLSEKPLISEETDLIEPTLLDEL
          KKPSETQELVQQVLSLA.QDSDNPDL.D.GYIYW.LL.TDPVTAK.VVLSEKPLISEETDL.EPTLLDEL
Retrocopy KKPSETQELVQQVLSLASQDSDNPDL*DWGYIYWCLLWTDPVTAK*VVLSEKPLISEETDLTEPTLLDEL

Parental  ICHIGSLASVYHKPPNAFVEGSHGIHRKHLPIHHGSTDAGDSPVGTTTATNLEQPQVIPSQGDLLGDLLN
          ICHIGSLASVYHKPPNAFVE.SH.IHRKHLPIHHGSTDAGDSPVGTT.A.NLEQPQVIPSQGDLLGDLLN
Retrocopy ICHIGSLASVYHKPPNAFVEESHVIHRKHLPIHHGSTDAGDSPVGTTIAMNLEQPQVIPSQGDLLGDLLN

Parental  LDLGPPVNVPQVSSMQMGAVDLLGGGLDSLLGSDLGGGIGGSPAVGQSFIPSSVPATFAPSPTPAVVSSG
          LDLGPPVNVPQVSSMQMGAVDLLGGGLDSLLG....GGIGGSPAVGQSFIPSSVP.TFAPSP.PAV.SSG
Retrocopy LDLGPPVNVPQVSSMQMGAVDLLGGGLDSLLG----GGIGGSPAVGQSFIPSSVPETFAPSPIPAVISSG

Parental  LNDLFELSTGIGMAPGGYVAPKAVWLPAVKAKGLEISGTFTHRQGHIYMEMNFTNKALQHMTDFAIQFNK
          LNDLFELSTGIG.AP.GYVAPKAVWLPAVKAKGLEISGTFTHRQGHIYMEMNFTNKALQHMTDFAIQFNK
Retrocopy LNDLFELSTGIGIAPSGYVAPKAVWLPAVKAKGLEISGTFTHRQGHIYMEMNFTNKALQHMTDFAIQFNK

Parental  NSFGVIPSTPLAIHTPLMPNQSIDVSLPLNTLGPVMKMEPLNNLQVAVKNNIDVFYFSCLIPLNVLFVED
          NSFGVIPSTPLAIHTPLMPNQSIDVSLPLNTLGPVMKMEPLNNLQVAVKNN.DVFYFSCLIPLNVLFVE.
Retrocopy NSFGVIPSTPLAIHTPLMPNQSIDVSLPLNTLGPVMKMEPLNNLQVAVKNNTDVFYFSCLIPLNVLFVEK

Parental  GKMERQVFLATWKDIPNENELQFQIKECHLNADTVSSKLQNNNVYTIAKRNVEGQDMLYQSLKLTNGIWI
          .KMERQVFLATWKDIPNENEL.FQIKECHLNADTVSSKLQNNNVYTIAKRNVEGQDMLYQSLKLTNGIWI
Retrocopy SKMERQVFLATWKDIPNENELHFQIKECHLNADTVSSKLQNNNVYTIAKRNVEGQDMLYQSLKLTNGIWI

Parental  LAELRIQPGNPNYTLSLKCRAPEVSQYIYQVYDSILK
          LAEL.IQPGNPNYTLSLKCRAP.VSQYI.QVYDSILK
Retrocopy LAELCIQPGNPNYTLSLKCRAP*VSQYISQVYDSILK

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	2.24 RPM	80.76 RPM
SRP051959_heart	2.14 RPM	79.46 RPM
SRP051959_kidney	2.46 RPM	82.58 RPM
SRP051959_liver	1.08 RPM	48.19 RPM
SRP051959_lung	2.93 RPM	121.63 RPM
SRP051959_lymph_node	2.90 RPM	108.65 RPM
SRP051959_skeletal_muscle	1.07 RPM	44.88 RPM
SRP051959_spleen	2.84 RPM	104.39 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1850 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1850 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1850 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020316	1 retrocopy	retro_btau_1675,
Choloepus hoffmanni	ENSCHOG00000010864	1 retrocopy	retro_chof_2310,
Callithrix jacchus	ENSCJAG00000014853	1 retrocopy	retro_cjac_1850 ,
Gorilla gorilla	ENSGGOG00000015593	1 retrocopy	retro_ggor_3044,
Loxodonta africana	ENSLAFG00000015777	1 retrocopy	retro_lafr_446,
Myotis lucifugus	ENSMLUG00000002837	1 retrocopy	retro_mluc_2443,
Mustela putorius furo	ENSMPUG00000014910	1 retrocopy	retro_mputfur_704,
Mus musculus	ENSMUSG00000035152	1 retrocopy	retro_mmus_2503,
Nomascus leucogenys	ENSNLEG00000013939	2 retrocopies	retro_nleu_1925, retro_nleu_2554,
Pongo abelii	ENSPPYG00000008188	1 retrocopy	retro_pabe_3793,
Pan troglodytes	ENSPTRG00000009021	1 retrocopy	retro_ptro_3248,
Rattus norvegicus	ENSRNOG00000009988	2 retrocopies	retro_rnor_1267, retro_rnor_574,