RetrogeneDB ID: retro_cjac_2336

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:47504728..47506012(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEPT11
• Ensembl ID: ENSCJAG00000014744
• Aliases: SEPT11, septin-11
• Description: None

Sequence

>retro_cjac_2336
ATGGCTGTGGCCATGCGGACACCGTCTAATGAAGAGCTTCGAAACTTGTCTTTGTCTGGCCATGTGGGATTTGACAGCCT
CCCTGACCAGCTGGTCAAGAAGTCTACTTCTCAAGGATTCTGTTTCAACATCCTTTGTGTTGGTGAGACAGGCATTGGTA
AATCCACATTAATGGACACTTTGTTCAACACCAAATATGAAAGTGACCCAGCTACTCACAATGAACCAGGTGTCCAGTTA
AAAGCCAGAAGTTACAAGCTTCAGGAAAGCAACGTACGGCTGAAGTTAACCATCGTTGACACAGTGGAATTTGGAGACCA
GATAAATAAAGATGACAGCTATAAGCTGATAGTAGAATATATTGACGCCCAGTTCGAGGCCTACGTGCAAGAGGAACTGA
AGATTAAACGATCTCTCTTCAACTACCATGACATGAAGATCCATGCCTGCCTCTACTTTATTGCCCCTACTGGACATTCA
CTAAAATCCCTGGATCTGGTCACCATGAAAAAGCTGGACAGTAAGGTGAACATCATCCCAATAATTGTGAAAGCTGACAC
CATTGCCAAGAAAGAGCTGCACAAATTCAAGAGCAAGATCATGAGTGAACTAGTCAGCAATGGGGTCCAGATATATCAGT
TCCCCACTGATGAGGAAACAGTGGCAAAGATTAACACAACGAGTGTCCATCTCCCATTTGCAGTGGTTGGCAGCACCGAA
GAGCTGAAGATTGGCAACAAGATGGCAAAGGCCAGGCAGTACCCTTGGGGTGTGGTGCAGGTTGAGAATGAAAACCATTG
TGATTTTGTGAAACTTCGAGAGATGCTGATCCTGGTGAACATGGAAGACTTGTGAGAGCAGACTCACACCCGCCACTACG
AACTGTACGGACGCTGTAAGCTTGAAGAGATGAGGTTCAAGGACACCGACCCTGACAGCAAACCCTTCAGTCTTCAGGAG
ACATATGAAGCAAAAAGGAATGAATTCCTGGGTGAACTGCAGAAGAAAGAAGAAGAAATGAGACAAATGTTTGTTATGAG
AGTGAAGGAGAAAGAAGCTGAACTTAAAGAGGCAGAGAAAGAGCTTCACGAGAAGTTTGACCTTTTAAAGTGGACACACC
AAGAAGAAAAGAAGAAAGTGGAAGACAAGAAGAAGGAGCTTGAGGAGAAAGTGAACAACTTCCAGAAGAAGAAAGCGGTG
GCTCAGTTACTACAGTCCCAGGCCCAGCAATCTGGGGCCCAGCAAACCAAGAAAGACAAGGATAAGAAAAATGCAAGCTT
CACA

Alignment

ORF - retro_cjac_2336 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.17 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVAVGRPSNEELRNLSLSGHVGFDSLPDQLVNKSTSQGFCFNILCVGETGIGKSTLMDTLFNTKFESDP
          MAVA...PSNEELRNLSLSGHVGFDSLPDQLV.KSTSQGFCFNILCVGETGIGKSTLMDTLFNTK.ESDP
Retrocopy MAVAMRTPSNEELRNLSLSGHVGFDSLPDQLVKKSTSQGFCFNILCVGETGIGKSTLMDTLFNTKYESDP

Parental  ATHNEPGVRLKARSYELQESNVRLKLTIVDTVGFGDQINKDDSYKPIVEYIDAQFEAYLQEELKIKRSLF
          ATHNEPGV.LKARSY.LQESNVRLKLTIVDTV.FGDQINKDDSYK.IVEYIDAQFEAY.QEELKIKRSLF
Retrocopy ATHNEPGVQLKARSYKLQESNVRLKLTIVDTVEFGDQINKDDSYKLIVEYIDAQFEAYVQEELKIKRSLF

Parental  NYHDTRIHACLYFIAPTGHSLKSLDLVTMKKLDSKVNIIPIIAKADTIAKNELHKFKSKIMSELVSNGVQ
          NYHD..IHACLYFIAPTGHSLKSLDLVTMKKLDSKVNIIPII.KADTIAK.ELHKFKSKIMSELVSNGVQ
Retrocopy NYHDMKIHACLYFIAPTGHSLKSLDLVTMKKLDSKVNIIPIIVKADTIAKKELHKFKSKIMSELVSNGVQ

Parental  IYQFPTDEETVAEINATMSVHLPFAVVGSTEEVKIGNKMAKARQYPWGVVQVENENHCDFVKLREMLIRV
          IYQFPTDEETVA.IN.T.SVHLPFAVVGSTEE.KIGNKMAKARQYPWGVVQVENENHCDFVKLREMLI.V
Retrocopy IYQFPTDEETVAKINTT-SVHLPFAVVGSTEELKIGNKMAKARQYPWGVVQVENENHCDFVKLREMLILV

Parental  NMEDLREQTHTRHYELYRRCKLEEMGFKDTDPDSKPFSLQETYEAKRNEFLGELQKKEEEMRQMFVMRVK
          NMEDL.EQTHTRHYELY.RCKLEEM.FKDTDPDSKPFSLQETYEAKRNEFLGELQKKEEEMRQMFVMRVK
Retrocopy NMEDL*EQTHTRHYELYGRCKLEEMRFKDTDPDSKPFSLQETYEAKRNEFLGELQKKEEEMRQMFVMRVK

Parental  EKEAELKEAEKELHEKFDLLKRTHQEEKKKVEDKKKELEEEVNNFQKKKAAAQLLQSQAQQSGAQQTKKD
          EKEAELKEAEKELHEKFDLLK.THQEEKKKVEDKKKELEE.VNNFQKKKA.AQLLQSQAQQSGAQQTKKD
Retrocopy EKEAELKEAEKELHEKFDLLKWTHQEEKKKVEDKKKELEEKVNNFQKKKAVAQLLQSQAQQSGAQQTKKD

Parental  KDKKNASFT
          KDKKNASFT
Retrocopy KDKKNASFT

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	20.75 RPM
SRP051959_heart	0.05 RPM	21.52 RPM
SRP051959_kidney	0.02 RPM	33.59 RPM
SRP051959_liver	0.02 RPM	12.67 RPM
SRP051959_lung	0.03 RPM	27.35 RPM
SRP051959_lymph_node	0.00 RPM	21.25 RPM
SRP051959_skeletal_muscle	0.02 RPM	19.24 RPM
SRP051959_spleen	0.02 RPM	33.91 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2336 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2336 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2336 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003906	1 retrocopy	retro_chof_1543,
Callithrix jacchus	ENSCJAG00000006122	1 retrocopy	retro_cjac_1501,
Callithrix jacchus	ENSCJAG00000012276	2 retrocopies	retro_cjac_1259, retro_cjac_3809,
Callithrix jacchus	ENSCJAG00000014744	1 retrocopy	retro_cjac_2336 ,
Callithrix jacchus	ENSCJAG00000017754	3 retrocopies	retro_cjac_1736, retro_cjac_2879, retro_cjac_828,
Monodelphis domestica	ENSMODG00000011825	1 retrocopy	retro_mdom_224,
Oryctolagus cuniculus	ENSOCUG00000001289	1 retrocopy	retro_ocun_1758,
Otolemur garnettii	ENSOGAG00000005210	1 retrocopy	retro_ogar_2831,
Pan troglodytes	ENSPTRG00000016192	1 retrocopy	retro_ptro_2753,