RetrogeneDB ID: retro_cjac_17

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:47192209..47195275(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000000609
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TSHZ1
• Ensembl ID: ENSCJAG00000003224
• Aliases: None
• Description: None

Sequence

>retro_cjac_17
GCAGGCTACGCCCAGGAGGAACAGCTGAAAGAAGAGGAGGAAATAAAAGAAGAGGAAGAAGAGGACAGTGGTTCAGTAGC
TCAACTGCAGGGTGGCAATGACACAGGGACAGACGAGGACCTAGAAACCGGCCCGGAGCAGAAAGGCTGCTTCAGCTACC
AGAACTCTCCAGGAAGTCATTTGTCCAATCAGGATGCCGAGAACGAGTCTCTGCTGAGCGACGCCAGCGATCAGGTGTCG
GACATCAAGAGCGTCTGCGGCCGAGATGCCTCGGACAAGAAAAGCAACACTCACGTCAAGCTTCCAAACGAAACACACAA
CTGCATGGACAAAATGACTGCGGTCTACGCCAACATCCTGTCTGATTCCTATTGGTCGGGCCTGGGCCTCGGCTTCAAGC
TGTCCAATAGTGAGAGGCGGCACTGTGACACCCGGAATGGCAGCAACAAGAGCGATTTTGATTGGCACCAAGACGCTCTG
TCCAAAAGCCTGCAGCAGAACTTGCCGGCCAGGTCCATCTCGAAACCCAGCCTGTTCAGCTCAGTGCAGCTGTATCGGCA
GAGCAGCAAGATGTGCGGGACTGTGTTCACCGGGGCCAGCCGATTCCGATGCCGGCAGTGCAGCGCTGCCTACGACACCC
TTGTGGAGCTGACCGTGCACATGAACGAAACGGGCCACTATCAAGATGACAACCGCAAGAAGGACAAGCTCAGACCTGCG
AGCTATTCAAAGCCCCGGAAGAGGGCTTTCCAGGATATGGACAAGGAGGATGCTCAGAAGGTTCTGAAATGTATGTTTTG
TGGCGACTCCTTCGATTCCCTCCAAGATTTGAGTGTCCACATGATTAAAACAAAACATTACCAAAAAGTGCCTTTGAAGG
AGCCAGTCCCAACCATTTCCTCGAAGATAGTCACCCCTGCGAAGAAGCGCGTTTTCGATGTCAATCGGCCGTGTTCCCCC
GATTCAACCACAGGATCTTTTGCAGATTCTTTTTCTTCCCAGAAGAACGCCAACTTGCAGTTGTCCTCCAACAACCGCTA
TGGCTACCAGAATGGAGCCAGCTACACCTGGCAGTTTGAGGCCTGCAAGTCCCAGATCTTAAAGTGCATGGAGTGTGGGA
GCTCCCATGACACCTTGCAGCAGCTCACCACCCACATGATGGTCACAGGTCACTTTCTCAAGGTCACCAGCTCTGCCTCC
AAGAAAGGGAAGCAGCTGGTGTTAGACCCGCTGGCTGTAGAGAAAATGCAGTCGTTGTCCGAGGCCCCAAACAGTGATTC
TCTGGCTCCCAAGCCATCCAGTAACTCAGCAGCAGACTGTACAGCCTCTACCACTGAGTTAAAGAAAGAGAGTAAAAAAG
AAAGGCCAGAGGAAACCAGCAAGGATGAGAAAGTCGTGAAAAGCGAGGACTATGAAGATCCTCTACAAAAACCTTTAGAC
CCTACAATCAAATATCAATATCTAAGGGAGGAGGACTTGGAAGATGGCTCAAAGGGTGGTGGGGACATTTTGAAATCTTT
GGAAAATACTGTCACCACAGCCATCAACAAAGCCCAAAATGGGGCCCCCAGCTGGAGTGCCTACCCCAGCATCCACGCAG
CCTATCAGCTGTCCGAGGGCACTAAGCCACCTTTGCCTATGGGATCCCAGGTACTGCAGATCCGGCCTAATCTCACCAAC
AAGCTGAGGCCCATTGCACCAAAGTGGAAAGTGATGCCACTCATTTCTGTGCCCACAAACCTGGCCCCTTACACTCAAGT
CAAGAGGGAGTCAGAAGACAAAGATGAAGTCGTGAAGGAGTGTGGGAAAGAAAGTCCCCATGAAGAGGCCTCATCTTTCA
GCCACAGTGAGGGCGATTCTTTCCGTAAAAGCGAAACGCCCCCAGAAGCCAGAAAGACTGAGCTGGGTCCCCTGAAGGAG
GAGGACAAGCTGATGAAAGAGGGCAGCGAAAAGGAGAAACCCCAGCCGCTGGAGCCCACTTCTGCTCTGAGCAACGGGTG
CGCCCTTGCCAACCACACCCCGGCCCTGCCATGTATCAACCCGCTCAGCGCCCTGCAGTCCGTCCTGAACAATCACCTGG
GCAAAGCCACAGAGCCCTTACGCTCACCTTCCTGCTCCAGCCCAAGTTCAAGCACAATTTCCATGTTCCACAAGTCGAAT
CTCAGTGTCATGGACAAACCAGTCTTGAGTCCCGCCTCCTCAAGGCCAGCTAGCGTATCCAGACGCTACCTGTTTGAGAA
CAACGATCAGCCCATTGACCTGACCAAGTCCAAAAGCAAGAAAGCCGAGTCCTCGCAAGCACAATCCTGTACGTCCCCAC
CTCAGAAGCATGCTCTGTCTGACATCGCAGACATGGTCAAAGTCCTCCCCAAAGCCACCACCCCAAAGCCCGCTGCTTCC
TCCAGGGTCCCTCCCATGAAGCTGGAAATGGACGTTAGGCGCTTTGAGGATGTCTCCAGTGAAGTCTCGACTTTGCATAA
AAGAAAAGGCCGGCAGTCCAACTGGAATCCTCAGCATCTTCTGATTTTACAAGCTCAGTTTGCCTCGAGCCTCTTCCAGA
CATCAGAGGGCAAATACCTGCTGTCCGATCTGGGCCCTCAAGAGCGTATGCAAATCTCGAAGTTTACGGGACTTTCAATG
ACCACTATCAGTCACTGGCTGGCTAACGTCAAGTACCAGCTTAGGAAAACAGGCGGGACAAAATTTCTAAAAAACATGGA
CAAAGGCCACCCCATCTTTTATTGCAGTGACTGTGCCTCCCAGTTCAGAACCCCTTCTACCTACATCAGTCACTTAGAAT
CTCACCTGGGTTTCCAAATGAAGGACATGACCCGCTTGTCAGTGGACCAGCAAAGCAAGGTGGAGCAAGAGATCTCCCGG
GTATCGTCGGCTCAGAGGTCTCCGGAAACAATAGCTGGTGAAGAGGACACAGACTCTAAATTCAAGTGTAAGTTGTGCTG
TCGGACATTTGTGAGCAAACATGCAGTAAAACTCCACCTAAGCAAAACGCACAGCAAGTCACCTGAACACCATTCACAGT
TTGTAACAGACGTGGATGAAGAATAG

Alignment

ORF - retro_cjac_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.96 %
• Parental protein coverage: 65.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EIKEAQSYQNSPVSSATNQDAGYGSPFSESSDQLAHFKGSSSREEKEDPQCPDSISYPQDS---LAQIKA
          E.K...SYQNSP.S...NQDA...S..S..SDQ....K....R....D.........P...........A
Retrocopy EQKGCFSYQNSPGSHLSNQDAENESLLSDASDQVSDIKSVCGRDAS-DKKSNTHVKLPNETHNCMDKMTA

Parental  VYANLFSESCWSSLALDLKKSGSTT---STNDASQKSGYDWHQAALAKTLQQTSSYGLLPEPSLFSTVQL
          VYAN..S.S.WS.L.L..K.S.S......T...S.KS..DWHQ.AL.K.LQQ.........PSLFS.VQL
Retrocopy VYANILSDSYWSGLGLGFKLSNSERRHCDTRNGSNKSDFDWHQDALSKSLQQNLPARSISKPSLFSSVQL

Parental  YRQNNKLYGSVFTGASKFRCKDCSAAYDTLVELTVHMNETGHYRDDNRDKDSEKTKRWSKPRKRSLMEME
          YRQ..K..G.VFTGAS.FRC..CSAAYDTLVELTVHMNETGHY.DDNR.KD.......SKPRKR....M.
Retrocopy YRQSSKMCGTVFTGASRFRCRQCSAAYDTLVELTVHMNETGHYQDDNRKKDKLRPASYSKPRKRAFQDMD

Parental  GKEDAQKVLKCMYCGHSFESLQDLSVHMIKTKHYQKVPLKEPVPAITKLVPSTKKRALQDLAPPCSPEVA
          .KEDAQKVLKCM.CG.SF.SLQDLSVHMIKTKHYQKVPLKEPVP.I........K....D...PCSP...
Retrocopy -KEDAQKVLKCMFCGDSFDSLQDLSVHMIKTKHYQKVPLKEPVPTISSKIVTPAKKRVFDVNRPCSPD--

Parental  GMATEVALSESAKDQKAANPYVTPNNRYGYQNGASYTWQFEARKAQILKCMECGSSHDTLQQLTAHMMVT
          ...T......S...QK.AN.....NNRYGYQNGASYTWQFEA.K.QILKCMECGSSHDTLQQLT.HMMVT
Retrocopy --STTGSFADSFSSQKNANLQLSSNNRYGYQNGASYTWQFEACKSQILKCMECGSSHDTLQQLTTHMMVT

Parental  GHFLKVTTSASKKGKQLVLDPVVEEKIQSIPLPPTTHTRLLASGIKKQPDSPAGSTASEEKKEPEKEKVP
          GHFLKVT.SASKKGKQLVLDP...EK.QS....P...............D..A..T..E.KKE..KE...
Retrocopy GHFLKVTSSASKKGKQLVLDPLAVEKMQSLSEAPNSDSLAPKPSSNSAADCTASTT--ELKKESKKERPE

Parental  VAGDTEKI--KEESEDSSEK-FEPSTLYPYLREEDLDDSPKGGVDILKSLENTVSTAISKAQNGAPSWGG
          .....EK....E..ED...K...P...Y.YLREEDL.D..KGG.DILKSLENTV.TAI.KAQNGAPSW..
Retrocopy ETSKDEKVVKSEDYEDPLQKPLDPTIKYQYLREEDLEDGSKGGGDILKSLENTVTTAINKAQNGAPSWSA

Parental  YPSIHAAYQL-PGTVKPLPAAVQSVQVQPSYAGGMKSLSSA-EHNALLHSPGSLTPPPHKSNVSAMEELV
          YPSIHAAYQL..GT..PLP...Q..Q..P.................L...P..L.P.......S.....V
Retrocopy YPSIHAAYQLSEGTKPPLPMGSQVLQIRPNLTNKLRPIAPKWKVMPLISVPTNLAPYTQVKRESEDKDEV

Parental  EKVTGKKEKSSPAKAGSPVAKENKDFPKTE-EVSGKQQKKGHEAESGKAKKEGPLDAHTPNGTEPLKAKV
          .K..GK...S....A.S....E...F.K.E..........G...E..K..KEG......P...EP..A..
Retrocopy VKECGK--ESPHEEASSFSHSEGDSFRKSETPPEARKTELGPLKEEDKLMKEGS-EKEKPQPLEPTSA-L

Parental  TNGCSNLGIITDHSPEPSFINPLSALQSIMNTHLGKVSKPV-SPS
          .NGC........H.P....INPLSALQS..N.HLGK...P..SPS
Retrocopy SNGCA----LANHTPALPCINPLSALQSVLNNHLGKATEPLRSPS

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	3.68 RPM	5.90 RPM
SRP051959_heart	5.53 RPM	8.23 RPM
SRP051959_kidney	2.15 RPM	11.49 RPM
SRP051959_liver	2.92 RPM	3.55 RPM
SRP051959_lung	7.09 RPM	9.26 RPM
SRP051959_lymph_node	7.31 RPM	9.57 RPM
SRP051959_skeletal_muscle	2.99 RPM	5.50 RPM
SRP051959_spleen	25.19 RPM	7.50 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_17 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_17 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_17 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003224	1 retrocopy	retro_cjac_17 ,
Ornithorhynchus anatinus	ENSOANG00000001135	1 retrocopy	retro_oana_3,