RetrogeneDB ID: retro_cjac_1529

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:94855161..94856850(-)
• Located in intron of: ENSCJAG00000015651

Retrocopy information

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

Parental gene information

• Parental gene symbol: LETM1
• Ensembl ID: ENSCJAG00000001859
• Aliases: None
• Description: None

Sequence

>retro_cjac_1529
GTATACTGCCCCACCCACCCCACAGACATGGTGGTGAAGAAGTCCCTCTGGCAGAGGTAGCTGGATGAGCTGAAGCACTA
CTGCTGTGGCTTCCACCTGCTGTGGAGCCACACCAAGATGGCGGTGCGCATGCTCTGGCACATCCTTGCCAGCCACACCC
TGACCAGCCAGGAGCGCAAGCAGTTTCTACGGATCTGCACCACCCCCTTTTGCTTGGTGCGGTTCCTCGTGTTTGTGGTG
GTCCAGTTCATGGAGTTCCTGCCGCCCATGACCTTGAGGTTCTTCCCCAACATGCCATCATTCACATTTGAGACCCAGTT
CATCAAGGAGGAGAGGCTGAAGAAGGAAGTTCAGGTCAACCTGGAGCTGGCGAAGTTCCTCCAGGACACCATCAAGAAGA
GGGTCTTGAAGAACCAGGCAGCCAAGGGCAGTGCCACCAGACTACTCTGTTTTTTCAGAAGATCTGGGAGATGGGGGAGA
GACCCAGCAATGAAGAAATCATGCGTTTTTTCAAATTATTTGAGAATAAGCTGACCCTGGACAACCTGTCATGGCCACAG
CTGATGGCACTGTGCATGCTGCTGGAGCTGCGGTCCGTTGACACCAACAACTTCTGTGCTTCCAGCTCACCATGCAGCTC
TGTTCCATAAAGGCCAACGGCAAGCCGATATCTAAGGAGGGGTGGACAGCCTGAATGTCAAGTAGCTGCAGGCAGTGTGT
GGGGAGGGAGGCATGTGAGTTATATGTCAATGTCAGTTGTCATCTGTTCAGCATCAGCTGAAGCAGTGGCTGGACCTGCA
CCTGCATCAAAAGATCCCCATATCTCTCCTCATCCTGTCCCAGGCTATGTACCTTCTAGACACCATCTCGCCAGCCAACC
AGCTCAAGTCCATACTGCAGTCCCTCCCAGAGACTGTGGCAAAGGAAGCACAGGTGAAAGCAGCCGAGATAGAGGGTGAG
TGGGTGGACAACAAGGCCAAGCCGGAGGCCATGCTATAGGAGGAGGAAGCTGTCCAGCAGGAGCACCACAAGAAGGAGCT
GCAGAAGTGCTCGGAGGTGGAAAAGGATGTCAAGCCTGAAGGTATGGAAGCCACTCCTCAAAGGCCAGGGGCCTCACTGC
AGCCAGAAGTGCTTGATGCAGTCCTGTGGTCAGAGACCCTGAAGGACGCTGCCCCACTGCTAGAGAGCTCTAACGAGGAA
GAAATAGCTAAGAAGGAAATAGGCATCCTCAGCAATGCCTGCTGTAAGCTCAAGGAGCAGAAGTTGCTCATCGAGGAGAA
GATGGAGCTGGAGCTGCTGAAGGAGGACATGCAGGACTACAGCAAGGACTTGCAAGAGATGAAGGAGGAACTTTCAAACA
CCAGTAAAGAAACTTATGTAGAAGAATCTAAAGCCAGCAAGATACTGACCAACAGGGTGCAGCAGATGATCAGGCAGATG
GAGGACTTGATCTTGCACCTGGAGATGGGCCAGCAGCTGGAAACTGGGCCTGGCCTAGGGCATGCCTCAGGGGAGAACAC
CATCACTGTCACTGAGCTCATCAGCACCACACTGTGAAGCAAGTCAGGCAGTCCAGAAAACAAGCTCACTAGCCTGGCCA
AAGCACTCGATGAAGACAAGAATGGCAAAGGCAGCACTGACAACCTTGTCAGCGTGATTGAGTTTGTAGACAAAGATGAT
GTAGAGATG

Alignment

ORF - retro_cjac_1529 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.56 %
• Parental protein coverage: 79.07 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VYSP--PAEVVVKKSLGQRVLDELKHYYHGFRLLWIDTKIAARMLWRILNGHTLTRRERRQFLRICADLF
          VY.P..P...VVKKSL.QR.LDELKHY..GF.LLW..TK.A.RMLW.IL..HTLT..ER.QFLRIC...F
Retrocopy VYCPTHPTDMVVKKSLWQR*LDELKHYCCGFHLLWSHTKMAVRMLWHILASHTLTSQERKQFLRICTTPF

Parental  RLVPFLVFVVVPFMEFLLPVAVKLFPNMLPSTFETQSIKEERLKKELRVKLELAKFLQDTI-EEMALKNK
          .LV.FLVFVVV.FMEFL.P.....FPNM...TFETQ.IKEERLKKE..V.LELAKFLQDTI..E..L...
Retrocopy CLVRFLVFVVVQFMEFLPPMTLRFFPNMPSFTFETQFIKEERLKKEVQVNLELAKFLQDTI<QEEGLEEP

Parental  AAKGSATKDFSVFFQKIRETGERPSNEEIMRFSKLFEDELTLDNLTRPQLVALCKLLELQSIGTNNF-LR
          ...G........FFQKI.E.GERPSNEEIMRF.KLFE..LTLDNL..PQL.ALC.LLEL.S..TNNF.L.
Retrocopy GSQGQCHQT-TLFFQKIWEMGERPSNEEIMRFFKLFENKLTLDNLSWPQLMALCMLLELRSVDTNNF<LC

Parental  FQLTMRLRSIKADDKLIAEEG-VDSLNVKELQAACRARGMRALGVTE-DRLRGQLKQWLDLHLHQEIPTS
          FQLTM.L.SIKA..K.I..EG.VDSLNVK.LQA.C...GM.............QLKQWLDLHLHQ.IP.S
Retrocopy FQLTMQLCSIKANGKPISKEG<VDSLNVK*LQAVCGEGGM*VICQCQLSSVQHQLKQWLDLHLHQKIPIS

Parental  LLILSRALYLPDTLSPADQLKSTLQTLPEIVAKEAQVKAAEVEGEQVDNKAKLEATLQEEAAIQQEHLEK
          LLILS.A.YL.DT.SPA.QLKS.LQ.LPE.VAKEAQVKAAE.EGE.VDNKAK.EA.L.EE.A.QQEH..K
Retrocopy LLILSQAMYLLDTISPANQLKSILQSLPETVAKEAQVKAAEIEGEWVDNKAKPEAML*EEEAVQQEHHKK

Parental  ELQRRSEAAKDLELESVEAAPRRAGAEPQPEVPDTVLQSETLKDTAPVLEGLKEEEITKEEIDILSDACS
          ELQ..SE..KD...E..EA.P.R.GA..QPEV.D.VL.SETLKD.AP.LE...EEEI.K.EI.ILS.AC.
Retrocopy ELQKCSEVEKDVKPEGMEATPQRPGASLQPEVLDAVLWSETLKDAAPLLESSNEEEIAKKEIGILSNACC

Parental  KLQEQKKSLTKEKEELELLKEDVQDYSQDLQEIKKELSKTGEEQYVEESKASKRLTKRVQQMIGQIDGLI
          KL.EQ.K.L..EK.ELELLKED.QDYS.DLQE.K.ELS.T..E.YVEESKASK.LT.RVQQMI.Q...LI
Retrocopy KLKEQ-KLLIEEKMELELLKEDMQDYSKDLQEMKEELSNTSKETYVEESKASKILTNRVQQMIRQMEDLI

Parental  SQLEMDQQAGKLAPAEGVPTGENVISVAELISAMKQVKH-IPESKLTSLAAALDENKDGRVNIDDLVKVI
          ..LEM.QQ.....P..G...GEN.I.V.ELIS.....K...PE.KLTSLA.ALDE.K.G....D.LV.VI
Retrocopy LHLEMGQQL-ETGPGLGHASGENTITVTELISTTL*SKSGSPENKLTSLAKALDEDKNGKGSTDNLVSVI

Parental  ELVDKEDVHV
          E.VDK.DV..
Retrocopy EFVDKDDVEM

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	0.71 RPM	12.07 RPM
SRP051959_heart	0.54 RPM	9.10 RPM
SRP051959_kidney	0.78 RPM	13.51 RPM
SRP051959_liver	0.41 RPM	8.66 RPM
SRP051959_lung	0.94 RPM	6.75 RPM
SRP051959_lymph_node	1.26 RPM	6.99 RPM
SRP051959_skeletal_muscle	0.13 RPM	12.05 RPM
SRP051959_spleen	1.05 RPM	7.52 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1529 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1529 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1529 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001859	1 retrocopy	retro_cjac_1529 ,
Homo sapiens	ENSG00000168924	1 retrocopy	retro_hsap_2019,
Gorilla gorilla	ENSGGOG00000002923	2 retrocopies	retro_ggor_1158, retro_ggor_1159,
Nomascus leucogenys	ENSNLEG00000000067	2 retrocopies	retro_nleu_1752, retro_nleu_2731,
Otolemur garnettii	ENSOGAG00000014883	1 retrocopy	retro_ogar_20,
Pongo abelii	ENSPPYG00000014533	1 retrocopy	retro_pabe_1655,
Ictidomys tridecemlineatus	ENSSTOG00000014167	1 retrocopy	retro_itri_160,