RetrogeneDB ID: retro_cjac_1930

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:81492352..81493606(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000008218
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SF1
• Ensembl ID: ENSCJAG00000002780
• Aliases: None
• Description: None

Sequence

>retro_cjac_1930
ACAGGAGACCTGGGCATCCCCCCTAACCCTGAGGACAAGTCCCCTTCCCCTGAGCCCATCTGCAATAGCGAGAGGAAGCG
GCTTAACACCCGAGAGTTCTGCACCCACAAAAAACTGGAAGAGGAGCGGCACCACCTCATCACTGAGATGGTTGCACTCA
ACCCGATTTTTAATCCACCTGCAGATTGCAAACTTCCAGCAACACGTGTGAGTGATAAAGTCATGGTTCCACAAGGTGAG
TACCCAGAAATCAACTTTGTGGGGCTGCTCATTGGACCCAGAGGGAACACCCTAAAGAACATAGAGGAGTGCAATGCCAA
GGTTATGTGATCCAGGGGAAAGGATCTGTGAAAGAAGGGAAGGTTGGGTGCAAAGACGGCCAGATGTTGCCGGGAAAAGA
GGAGCCACTTCATGCCCTGGTCACCACCAATACAATGGAGAACGTCAAAAAGGCAGTGGAACAGATAAGAAACATCTTGA
AGCAGGGTATCGAGACCCCAGAAGACCAGAATGATCTACGGAAGATGCAGCTTCAGGAGTTGGCTTGCTTGAATGGGACC
CTTTGGGAAGACGACCACAGGATCTTAAGACCCTGGCAGATTTCAGAGACCTGCAGCATTACCAACACCACAGTGCGTAC
CAGGTGTGGAGGGGCTGGCCACATCACTTCAGACTGCAAATTCCAAAGGCCTGGTGATCCCCAGTCAGCTCAGGATAAAG
CACGGATGGATAAAGAATATTTGTCCCTCACAGCTGAACTGGGTGAAGCACCTGTCCCAGCATCTGTGGGCTCCACCTCT
GAGCCTGCCACCACACCCCTGGCCAGTGCACCTCGTCCTGCTGCTCCCGCCAGCAACCCACCTCCACCATGTCTCATGTC
CACCACCCAGAGCCGCCCAGCCTGGATGAATTCTGGCTCTTCAGAGAGTCAGCCTTACCACGGCATGAATGGAGGTAGTC
CTGATGGGCCTGGAGGCAGCCCCCATAGCTTCCCACACCCATTACCCAGCCTGACAGGTGGGCATGGCGGACATCCCATG
CAACATAACCCAATGGACCTCCACCCCTTTGGAAGCAGCCACCACCACCCTCGATGGACCAGGACTGCCACCCACCTGAG
CACCATGGCCCTCTCCAGTGGATCAGTACCTGGGAAGTAAACCGGTGGGCTCTGGGGTCTATCACCTGCATCAAGGAAAA
GGTATGATGCCGCCGCTGCTGCCGCCTCCCAGTGGACAGCCCCCGCCCCTCCCT

Alignment

ORF - retro_cjac_1930 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.58 %
• Parental protein coverage: 68.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TGDLGIPPNPEDRSPSPEPIYNSEGKRLNTREFRTRKKLEEERHNLITEMVALNPDFKPPADYKPPATRV
          TGDLGIPPNPED.SPSPEPI.NSE.KRLNTREF.T.KKLEEERH.LITEMVALNP.F.PPAD.K.PATRV
Retrocopy TGDLGIPPNPEDKSPSPEPICNSERKRLNTREFCTHKKLEEERHHLITEMVALNPIFNPPADCKLPATRV

Parental  SDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIM-IRG-KGSVKEGKVGRKDGQMLPGEDEPLH
          SDKVM.PQ.EYPEINFVGLLIGPRGNTLKNIE.ECNAK.M..RG.KGSVKEGKVG.KDGQMLPG..EPLH
Retrocopy SDKVMVPQGEYPEINFVGLLIGPRGNTLKNIE-ECNAKVM*SRG<KGSVKEGKVGCKDGQMLPGKEEPLH

Parental  ALVTANTMENVKKAVEQIRNILKQGIETPEDQNDLRKMQLRELARLNGTLREDDNRILRPWQSSETRSIT
          ALVT.NTMENVKKAVEQIRNILKQGIETPEDQNDLRKMQL.ELA.LNGTL.EDD.RILRPWQ.SET.SIT
Retrocopy ALVTTNTMENVKKAVEQIRNILKQGIETPEDQNDLRKMQLQELACLNGTLWEDDHRILRPWQISETCSIT

Parental  NTTVCTKCGGAGHIASDCKFQRPGDPQSAQDKARMDKEYLSLMAELGEAPVPASVGSTSGPATTPLASAP
          NTTV.T.CGGAGHI.SDCKFQRPGDPQSAQDKARMDKEYLSL.AELGEAPVPASVGSTS.PATTPLASAP
Retrocopy NTTVRTRCGGAGHITSDCKFQRPGDPQSAQDKARMDKEYLSLTAELGEAPVPASVGSTSEPATTPLASAP

Parental  RPAAPANNPPPPSLMSTTQSRPPWMNSGPSESRPYHGMHGGGPGGPGGGPHSFPHPLPSLTGGHGGHPMQ
          RPAAPA.NPPPP.LMSTTQSRP.WMNSG.SES.PYHGM.GG.P.GPGG.PHSFPHPLPSLTGGHGGHPMQ
Retrocopy RPAAPASNPPPPCLMSTTQSRPAWMNSGSSESQPYHGMNGGSPDGPGGSPHSFPHPLPSLTGGHGGHPMQ

Parental  HN-PNGPPPPWMQPPPPPMNQGPHPPGHHG-PPPMDQYLGSTPVGSGVYRLHQGKGMMPP--PPMGMMPP
          HN.PNGPPP.W.QPPPP.M.Q..HPP.HHG.P.P.DQYLGS.PVGSGVY.LHQGKGMMPP..PP....PP
Retrocopy HN<PNGPPPLWKQPPPPSMDQDCHPPEHHG<PSPVDQYLGSKPVGSGVYHLHQGKGMMPPLLPPPSGQPP

Parental  PPP
          P.P
Retrocopy PLP

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	0.00 RPM	24.43 RPM
SRP051959_heart	0.00 RPM	36.94 RPM
SRP051959_kidney	0.00 RPM	32.52 RPM
SRP051959_liver	0.00 RPM	23.48 RPM
SRP051959_lung	0.00 RPM	45.42 RPM
SRP051959_lymph_node	0.00 RPM	50.07 RPM
SRP051959_skeletal_muscle	0.02 RPM	35.31 RPM
SRP051959_spleen	0.02 RPM	37.84 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1930 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1930 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1930 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017828	1 retrocopy	retro_amel_1763,
Canis familiaris	ENSCAFG00000014239	1 retrocopy	retro_cfam_2148,
Callithrix jacchus	ENSCJAG00000002780	1 retrocopy	retro_cjac_1930 ,
Callithrix jacchus	ENSCJAG00000006580	1 retrocopy	retro_cjac_1185,
Callithrix jacchus	ENSCJAG00000012368	1 retrocopy	retro_cjac_3262,
Ictidomys tridecemlineatus	ENSSTOG00000009790	1 retrocopy	retro_itri_698,