RetrogeneDB ID: retro_cjac_1233

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:83426039..83427056(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUCLA2
• Ensembl ID: ENSCJAG00000009278
• Aliases: None
• Description: None

Sequence

>retro_cjac_1233
GTTGCCTCAACTTTCTCTCCAGAAGAAACAAAAGCTGTTTCCTCACAAATGATTGGGAAAAAGTTGTTTACCAAGCAAAT
GGGAGAAAAGGGCAGAATATGCTATCAAGCACTGGAGTGAAAATACCCCAGGAGAGAACACTACTTTGCAATTAACAATG
GGAAGGTCATTTCAAGGTCCTGTATTAACAGGGAGTTCACATGGTGGTGTCAACATTGCAGATGTTGCTGCGGAGACTCC
TGATGCAATTAAAGAACTGTTGATATTGTAGAAGGCATCAAAAAGGAACAAGCTCTCTGGTTTGAACAGAAGATGGGATT
TTCACCTGATATTGTGAATTCTGCAGCAGAAAACATGGTCAAGCTTTACAGCCTTTTTCTGAAATATGATGCAACCCTAG
TAAGAAATAAATCCAGTGGTGGAAGATTCAGATGGAGCTGTGCTATGCTGGATGCAAAGATCAATTTTGACTCTAATTCA
GCCTATCGCAAAAAGAAAATCCTTAATCTATAGGACTGAATCCAGGAAGATGAAAGTGACAAAGATGCTGCTAAGGCAGA
TCTCAATTACACTGGCCTCGATGGAACTACAGACTGTCTAGTACATGGTGCTAGTTTGGCCATGGCCACAATGGATATAA
ATAAAACTTCATGGAGGAACTCCAGCCAACTTCCTTATGTTGGCGGTGGTGCTACAGTCCATCAAGTAACAGAAGCATTT
AAGCTTATCGCTTCAGAAAAAAAGGTACTGACTACTCTGGTCAACATTTTTGGAGAAATCATGCACTGCGATGTTACTGC
ACAGGTTATAGTTGTGGCAGTAAAAGATGTGGAAATCAAAATCCTGTTGTGGTACAGGGTACAAGGTATACGAGTTGATG
ATGAGGCACTGAGAGTGGGCAGTGGGCTTAAAATTCTTGCTTGTGATGACTTGGAGGAAGCTGCTAGAATGGTCAGAAAG
CTCTCTGAAATAGTGACCTTAACCAAGCAAGTACATGTGGATGTGAAATTTCAGTTG

Alignment

ORF - retro_cjac_1233 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.8 %
• Parental protein coverage: 84.69 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  VKIVFSPEEAKAVSSQMIGKKLFTKQTGEKGRICNQVLVCERKYPRREYYFAI-TMERSFQGPVLIGSSH
          V...FSPEE.KAVSSQMIGKKLFTKQ.GEKGRIC.Q.L..E.KYPRRE.YFAI.TM.RSFQGPVL.GSSH
Retrocopy VASTFSPEETKAVSSQMIGKKLFTKQMGEKGRICYQAL--E*KYPRREHYFAI>TMGRSFQGPVLTGSSH

Parental  GGVNIEDVAAETPEAIIKE-PIDIVEGIKKEQALRLAQKMGFPPNIVDSAAENMVKLYSLFLKYDATMI-
          GGVNI.DVAAETP.AI.KE...DIVEGIKKEQAL...QKMGF.P.IV.SAAENMVKLYSLFLKYDAT...
Retrocopy GGVNIADVAAETPDAI-KE<TVDIVEGIKKEQALWFEQKMGFSPDIVNSAAENMVKLYSLFLKYDATLV>

Parental  EINPMVEDSDGAVLC-MDAKINFDSNSAYRQKKIFDLQDWTQEDERDKDAAKANLNYIGLDGNIGCLVNG
          EINP.VEDSDGAVLC..DAKINFDSNSAYR.KKI..L.D..QEDE.DKDAAKA.LNY.GLDG...CLV.G
Retrocopy EINPVVEDSDGAVLC<LDAKINFDSNSAYRKKKILNL*D*IQEDESDKDAAKADLNYTGLDGTTDCLVHG

Parental  AGLAMATMDI-IKLHGGTPANFL-DVGGGATVHQVTEAFKLITSDKKVLAILVNIFGGIMRCDVIAQGIV
          A.LAMATMDI.IKLHGGTPANFL..VGGGATVHQVTEAFKLI.S.KKVL..LVNIFG.IM.CDV.AQ.IV
Retrocopy ASLAMATMDI>IKLHGGTPANFL<YVGGGATVHQVTEAFKLIASEKKVLTTLVNIFGEIMHCDVTAQVIV

Parental  MAVKDLEIRIPVVVRLQGTRVDDAKALRADSGLKILACDDLDEAARMVVKLSEIVTLAKQAHVDVKFQL
          .AVKD.EI.I....R.QG.RVDD..ALR..SGLKILACDDL.EAARMV.KLSEIVTL.KQ.HVDVKFQL
Retrocopy VAVKDVEIKILLWYRVQGIRVDD-EALRVGSGLKILACDDLEEAARMVRKLSEIVTLTKQVHVDVKFQL

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	23.03 RPM
SRP051959_heart	0.12 RPM	51.94 RPM
SRP051959_kidney	0.13 RPM	39.36 RPM
SRP051959_liver	0.00 RPM	16.98 RPM
SRP051959_lung	0.02 RPM	16.48 RPM
SRP051959_lymph_node	0.00 RPM	14.31 RPM
SRP051959_skeletal_muscle	0.11 RPM	61.52 RPM
SRP051959_spleen	0.02 RPM	18.49 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1233 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1233 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1233 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014610	2 retrocopies	retro_acar_26, retro_acar_52,
Callithrix jacchus	ENSCJAG00000009278	2 retrocopies	retro_cjac_1233 , retro_cjac_2379,
Cavia porcellus	ENSCPOG00000014961	1 retrocopy	retro_cpor_1113,
Homo sapiens	ENSG00000136143	3 retrocopies	retro_hsap_2236, retro_hsap_2281, retro_hsap_3445,
Gorilla gorilla	ENSGGOG00000008224	3 retrocopies	retro_ggor_1668, retro_ggor_1694, retro_ggor_2327,
Macaca mulatta	ENSMMUG00000007539	1 retrocopy	retro_mmul_1231,
Mustela putorius furo	ENSMPUG00000001488	1 retrocopy	retro_mputfur_768,
Nomascus leucogenys	ENSNLEG00000002948	3 retrocopies	retro_nleu_1963, retro_nleu_2140, retro_nleu_2302,
Otolemur garnettii	ENSOGAG00000007452	1 retrocopy	retro_ogar_2196,
Pongo abelii	ENSPPYG00000005352	2 retrocopies	retro_pabe_1939, retro_pabe_2852,
Pan troglodytes	ENSPTRG00000005859	3 retrocopies	retro_ptro_1581, retro_ptro_1615, retro_ptro_2337,