RetrogeneDB ID: retro_cjac_1649

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:43994483..43995781(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBB2A
• Ensembl ID: ENSCJAG00000017637
• Aliases: None
• Description: tubulin, beta 2A class IIa [Source:HGNC Symbol;Acc:12412]

Sequence

>retro_cjac_1649
CCAGTCGGGCACAACCAGGTCGGTGCCAAGTTTTGGGAGGCCATCAGCGATGAGCATGGGATCGACCCCACAGGCAGTTA
TCATGGAGACAGTGACTTGCAGCTGGAGAGAATCAACATGTACTACAATGAGTCTGCTGGTAACAAATATGTACCTCGGG
CCATCCTGGTGGATCTGGAGCCTGGCACCATGGACTCCATCAGGTCTGGACCCTTCGGCCAGATCTTCAGGCCAAACAAC
TTTGTGTTCAGCCAGAGCAAAGCCGGGAATAACTGGGCCAAGGACCACTACACAGAGGGAGCCAAGCTAGTTGACTCAGT
CCTCAACATAGTGAGTCAGGGAGCTGTGATTGTCTCCAGGGCTTCCAGCTGACCCACTCTCTGGGGGGAAGCACAGGGTC
TGGGATGGGCACCCTGCTCATCAATCAGCAAGATCCAGGATGAGTATCCAGACTGCATCATGGACACCTTCAGCGTCATG
CCCTAACCCAAAGTGTCAGGCACGGCAGTGGAGCCCTACAATGCCACCTTCTCCGTCCACCAGCTGGTGGAAAACACAGA
TGAAACCTACTCCATTGATAATGAGGCCCTGTAGGACATCTGCTTCTGCACATTGAAGCTGACCACCCCCACCTACAGGG
ACCTCAACCACCTGGTGTTGGCCACTATGAGCAGGGTCACCACCTGCCTGCGCTTCCCAGGCCAGCTGAACACAGACCTG
CGCAAGCTGGCATGAACATGGTGCCCTTCCCACACCCGCAATTCTTCATGCTGGCTCAGTGCCCCTGACCAGCCGGGGCA
AGCCAGCAGTACCGCGCGCTCACAGTGCCCGAGCTCACCCAGCAGATGTTCAACTCCAAGAACAGGATGGTCACCTGCAA
CCCGGGCCATGGCCGCTACCTGACGGTGGCTGCCATCTTCTGGGGATGCATGTCCATGAAGGATGTGGACGAGCAGATGC
TCAACATGCAGAACAAGAACAGCAGCTACTTCGTGGAGTGTATTCCCAACAACATGAAGACAGCCATGTGTGACATCCCA
CCCCATGGCCTGAAGATGTCAGCCACCTTCATGTGCAACAGCACGGCCATCCAGGAGCTATTCAAGTACACCTCAGAGCA
GTTCACGGTCGTGCTCCGGCACAAGGCCTTCCTGCCCTGGTTCACCGGCAAGGGCATGGATGAGATGGAGTTCACCGAGG
CCGAGAGAAACATGAAGGACCTGGTTTCTGAGTACCATCAGGATGCCACGACCGACGAACAAGGGGAGTTCCAGGAGGAG
GAGAAGGGCGAGGACAAG

Alignment

ORF - retro_cjac_1649 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.92 %
• Parental protein coverage: 98.19 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PASGNHMGPKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYVPRAILVDLEPGTMDSVRSG
          P...N..G.KFWE.ISDEHGIDPTGSYHGDSDLQLERIN.YYNE..GNKYVPRAILVDLEPGTMDS.RSG
Retrocopy PVGHNQVGAKFWEAISDEHGIDPTGSYHGDSDLQLERINMYYNESAGNKYVPRAILVDLEPGTMDSIRSG

Parental  PFGQIFRPDNFVFAQSGAGNNWA-KGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSL-GGGTGSGM
          PFGQIFRP.NFVF.QS.AGNNWA..G....G.....S.L.....ES.SCDCLQGFQLTHSL.G...G.G.
Retrocopy PFGQIFRPNNFVFSQSKAGNNWA<QGPLHRGSQA--S*LSPQHSESGSCDCLQGFQLTHSL>GEAQGLGW

Parental  GTLL-ISKIREEYPDRIMNTFSVMPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLK
          .....ISKI..EYPD.IM.TFSVMP.PKVS.T.VEPYNAT.SVHQLVENTDETY.IDNEAL.DICF.TLK
Retrocopy APCSSISKIQDEYPDCIMDTFSVMP*PKVSGTAVEPYNATFSVHQLVENTDETYSIDNEAL*DICFCTLK

Parental  LTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLA-VNMVPFPRLHFFM-PGFAPLTSRG-SQQYRA
          LTTPTY.DLNHLV.ATMS.VTTCLRFPGQLN.DLRKLA..NMVPFP...FFM..G..PLTSRG.SQQYRA
Retrocopy LTTPTYRDLNHLVLATMSRVTTCLRFPGQLNTDLRKLA<MNMVPFPHPQFFM<AGSVPLTSRG>SQQYRA

Parental  LTVPELTQQMFDSKNMMAACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAV
          LTVPELTQQMF.SKN.M..C.P.HGRYLTVAAIF.G.MSMK.VDEQMLN.QNKNSSYFVE.IPNN.KTA.
Retrocopy LTVPELTQQMFNSKNRMVTCNPGHGRYLTVAAIFWGCMSMKDVDEQMLNMQNKNSSYFVECIPNNMKTAM

Parental  CDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQ
          CDIPP.GLKMSATF..NSTAIQELFK..SEQFT...R.KAFL.W.TG.GMDEMEFTEAE.NM.DLVSEY.
Retrocopy CDIPPHGLKMSATFMCNSTAIQELFKYTSEQFTVVLRHKAFLPWFTGKGMDEMEFTEAERNMKDLVSEY-

Parental  QYQDATADEQGEFEEEE-GEDE
          ..QDAT.DEQGEF.EEE.GED.
Retrocopy -HQDATTDEQGEFQEEEKGEDK

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	0.73 RPM	13.20 RPM
SRP051959_heart	0.28 RPM	9.05 RPM
SRP051959_kidney	0.02 RPM	6.28 RPM
SRP051959_liver	0.13 RPM	2.66 RPM
SRP051959_lung	1.50 RPM	13.08 RPM
SRP051959_lymph_node	0.07 RPM	1.60 RPM
SRP051959_skeletal_muscle	0.11 RPM	3.54 RPM
SRP051959_spleen	0.00 RPM	3.11 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1649 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1649 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1649 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004826	2 retrocopies	retro_cjac_1632, retro_cjac_2667,
Callithrix jacchus	ENSCJAG00000010101	1 retrocopy	retro_cjac_800,
Callithrix jacchus	ENSCJAG00000010530	1 retrocopy	retro_cjac_1144,
Callithrix jacchus	ENSCJAG00000011697	1 retrocopy	retro_cjac_3284,
Callithrix jacchus	ENSCJAG00000017637	1 retrocopy	retro_cjac_1649 ,
Myotis lucifugus	ENSMLUG00000016179	1 retrocopy	retro_mluc_401,
Tupaia belangeri	ENSTBEG00000004854	9 retrocopies	retro_tbel_2291, retro_tbel_3456, retro_tbel_3944, retro_tbel_4113, retro_tbel_413, retro_tbel_4390, retro_tbel_4439, retro_tbel_961, retro_tbel_962,
Tarsius syrichta	ENSTSYG00000003440	2 retrocopies	retro_tsyr_1068, retro_tsyr_2125,