RetrogeneDB ID: retro_cjac_510

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:26354580..26355418(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM98A
• Ensembl ID: ENSCJAG00000003525
• Aliases: None
• Description: family with sequence similarity 98, member A [Source:HGNC Symbol;Acc:24520]

Sequence

>retro_cjac_510
TATGAAGTCTGGAGAAAGTTGCTTATAAAACGTTTGGATGTCACTGTACAGTCTTTGAGCTGGTCTGACAGAGCTAAAAG
TCAGACAGAAAAATTAGCCAAGGTTTACCAGTTGAAAAGTTTTTCCTGTACCCTAAAAGTACTATTTCTGTTGCCCATCT
TTTGGCTGCAAGACAGCACTTGTAAAAGATTTTAAGGACAAGCAGCGGCTCTATAAGAGAAGACTGTGGTGCCATCAATA
AGGTGTTGATGGGCAAGGTGCCTGACAGAGGTGGCAGACCCAATGAAATCAAACCTCCACTCCCAGAGATGCCACCATGG
CAGAAGCGGCAAGATAGCCCCAGCAGCAAACAGAAGGCCGAGGAGGAGGAAGAGGTGGTTATGAATATTCCTCATATGCA
GGACCAGAAGGTCGTGAACAAGGAGGCGGGAGAGGTGGACGTGGCGGCTATGACCATGGTGGCCAAGGGGGAGGAAGAGG
AAATAACTAAAAAAGAGGCTGGACAGATGGAGTGGAGGAGAAGGTAGCTACCAAGATGGTGGCTATGGAGATTCAGGTTT
CCAGCCAGGTGGCTATTATGGTGGCCACAGTGGCGGCTATCAAGGTAGAGGTTATGGTGGATTTCAGACATATTCATATA
TAGGAAGCAGATACCAGGGTGGTGGCTACCAGCAGGATAATAGATACCAAGATGGCGGGCACCAAGGTGATTGTGGCAGT
GGTGAGAGCACCTTGTGGAGGGCAAGGTGGTTGTGCTGATCAGAGAGGAGGCTGGGGAGGAAGAGGGAGACAGAATTATC
ACCAAGGGGGTCAATATGAACAGCATTTCCAGCACGGG

Alignment

ORF - retro_cjac_510 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.85 %
• Parental protein coverage: 55.13 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  YEVRRKLLIKRLDVTVQSFGWSDRAKSQTEKLAKVYQPK-RSVLSPKSTISVAHLLAARQDLSKILRTSS
          YEV.RKLLIKRLDVTVQS..WSDRAKSQTEKLAKVYQ.K....L.PKSTISVAHLLAARQ.L.KILRTSS
Retrocopy YEVWRKLLIKRLDVTVQSLSWSDRAKSQTEKLAKVYQLK<KFFLYPKSTISVAHLLAARQHL*KILRTSS

Parental  GSIREKTACAINKVLMGRVPDRGGRPNEIEPPPPEMPPWQKRQDGP-QQQTGGRGGGRGGYEHSSYGGRG
          GSIRE....AINKVLMG.VPDRGGRPNEI.PP.PEMPPWQKRQD.P.QQQT.GRGGGRGGYE.SSY.G..
Retrocopy GSIREDCG-AINKVLMGKVPDRGGRPNEIKPPLPEMPPWQKRQDSP<QQQTEGRGGGRGGYEYSSYAGPE

Parental  GHEQGGGRGGRGGYDHGGRGG-GRGNKHQGGWTDGGSGGGGGYQDGGYRDSGFQPGGYHGGHSGGYQGGG
          G.EQGGGRGGRGGYDH.G..G.GR..K......D..SGG.G.YQDGGY.DSGFQPGGY.GGHSGGYQG.G
Retrocopy GREQGGGRGGRGGYDH-GGQG<GRKRK*LKKRLDRWSGGEGSYQDGGYGDSGFQPGGYYGGHSGGYQGRG

Parental  YGGFQTSSYTGSGYQGGGYQQDNRYQDGGHHGDRGGG-RGGRGGRGGRGGRAGQGGGWGGRGSQNYHQGG
          YGGFQT.SY.GS.YQGGGYQQDNRYQDGGH.GD.G.G.R...GG.GG....A.Q.GGWGGRG.QNYHQGG
Retrocopy YGGFQTYSYIGSRYQGGGYQQDNRYQDGGHQGDCGSG>RAPCGGQGG---CADQRGGWGGRGRQNYHQGG

Parental  QFEQHFQHG
          Q.EQHFQHG
Retrocopy QYEQHFQHG

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	18.15 RPM
SRP051959_heart	0.00 RPM	17.47 RPM
SRP051959_kidney	0.02 RPM	18.35 RPM
SRP051959_liver	0.00 RPM	14.36 RPM
SRP051959_lung	0.00 RPM	15.52 RPM
SRP051959_lymph_node	0.00 RPM	17.97 RPM
SRP051959_skeletal_muscle	0.00 RPM	18.65 RPM
SRP051959_spleen	0.00 RPM	17.37 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_510 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_510 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_510 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005268	2 retrocopies	retro_amel_1607, retro_amel_1845,
Callithrix jacchus	ENSCJAG00000003525	1 retrocopy	retro_cjac_510 ,