RetrogeneDB ID: retro_cjac_3809

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL284733.1:11027..12049(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEPT7
• Ensembl ID: ENSCJAG00000012276
• Aliases: None
• Description: None

Sequence

>retro_cjac_3809
GAACAATTCAAAGTTTTAATCAAAGAAGGTGGTGTTCAGTCGCTGTTCACAGTAGTTGATATCCTAGGATTTGGAGATGC
AGTGGATAATAGTAACTGCTGGCAGCCTGTTATCGACTACATTGCTAGTACATTTGAGGACTACCTAAATGCAGAATCGT
GAGTGGACAGACGTCAGATGCCTGAAAACAGGGCCCAGCATTGCTTATACTTCACTGCTCCTTCAGGACATGGACTTAAA
CCATTGGCTGCTGGGTTTCTGAAGCATTTGCATGAAAAAGTGACTATCATCTACTTATTGCCAAAGCAGACACACTCACA
CCAGAGGCATGCCAACGGTTTAAAAAACAGATAATGAAAGAAATCCAAGAACATAAAATTAAAATAAATGCATTTCCAGA
AACAGATGATGAAGAAGAAAATAAACTTGTTCAAAACATAAAGGACCATTTACCTCTTGCTGTGGTCGGTAGTAATACTA
TCATTGAAGTTAATGGCAAAAGGGTCAGAGGAAGGCAGTATCCTTGGGGTGTCGCTGAAGTTGAAAATGGTGAACACTGT
AATTTTACAATTCTAAGAGATCCATTGATAAGAACACATGTAGGACTTGAAAGATGTACTAATAATGTTCACTATGAGAA
CTACAGAAGCTGAAAACTGGCAGCTGTGACTTATAGTGGAGTCGGTAACAAGAAGAATAAGGGCAGCTGACTACGAGCCC
CTAGCACAGATGGAAGAAGAAAGAAGGGGGCATGTAGCTAAAATGAAGAAGATGGAGATGGAGATGGAGCCGTTGTTTGA
GATGAAGGTCGAAGAAAAAGTTCAAAAACTGAAGGACTCTGAAGCTGAGCTCCAGCGGCGCGAGGAGCAAATGACAAGAA
TTTGGAAGCACAGCACAAAGAATTAGAGGAAAACCGTCGTCAGTTTGAGGATGAGGAAGCAAACTGGGAAACTCAACGAC
GTATTTTAGAACCACAGAACTCTTCGAGAACCTTGGAGTAAAACAAGAAGAAAGGGAAGATC

Alignment

ORF - retro_cjac_3809 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.27 %
• Parental protein coverage: 89.32 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EQSKVLIKEGGVQLLLTIVDTPGFGDAVDNSNCWQPVIDYIDSKFEDYLNAESRVNRRQMPDNRVQCCLY
          EQ.KVLIKEGGVQ.L.T.VD..GFGDAVDNSNCWQPVIDYI.S.FEDYLNAES.V.RRQMP.NR.Q.CLY
Retrocopy EQFKVLIKEGGVQSLFTVVDILGFGDAVDNSNCWQPVIDYIASTFEDYLNAES*VDRRQMPENRAQHCLY

Parental  FIAPSGHGLKPLDIEFMKRLHEKVNIIPL-IAKADTLTPEECQQFKKQIMKEIQEHKIKIYEFPETDDEE
          F.APSGHGLKPL...F.K.LHEKV.II.L.IAKADTLTPE.CQ.FKKQIMKEIQEHKIKI..FPETDDEE
Retrocopy FTAPSGHGLKPLAAGFLKHLHEKVTIIYL<IAKADTLTPEACQRFKKQIMKEIQEHKIKINAFPETDDEE

Parental  ENKLVKKIKDRLPLAVVGSNTIIEVNGKRVRGRQYPWGVAEVENGEHCDFTILRNMLIRTHMQDLKDVTN
          ENKLV..IKD.LPLAVVGSNTIIEVNGKRVRGRQYPWGVAEVENGEHC.FTILR..LIRTH...L...TN
Retrocopy ENKLVQNIKDHLPLAVVGSNTIIEVNGKRVRGRQYPWGVAEVENGEHCNFTILRDPLIRTHV-GLERCTN

Parental  NVHYENYRSRKLAAVTYNGVDNNKNK-GQLTKS-PLAQMEEERREHVAKMKKMEMEMEQVFEMKVKEKVQ
          NVHYENYRS.KLAAVTY.GV.N.KNK.GQLT.S.PLAQMEEERR.HVAKMK.........FEMKV.EKVQ
Retrocopy NVHYENYRS*KLAAVTYSGVGNKKNK<GQLTTS<PLAQMEEERRGHVAKMKXXXXXXXPLFEMKVEEKVQ

Parental  KLKDSEAELQRRHEQM-KKNLEAQHKELEEKRRQFEDEKANWEAQQRILEQQNSSRTLEKNKKKGKI
          KLKDSEAELQRR.EQM..KNLEAQHKELEE.RRQFEDE.ANWE.Q.RILE.QNSSRTLE.NKKKGKI
Retrocopy KLKDSEAELQRREEQM<DKNLEAQHKELEENRRQFEDEEANWETQRRILEPQNSSRTLE*NKKKGKI

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	43.27 RPM
SRP051959_heart	0.02 RPM	72.07 RPM
SRP051959_kidney	0.11 RPM	54.07 RPM
SRP051959_liver	0.00 RPM	31.43 RPM
SRP051959_lung	0.00 RPM	78.86 RPM
SRP051959_lymph_node	0.00 RPM	68.10 RPM
SRP051959_skeletal_muscle	0.00 RPM	38.63 RPM
SRP051959_spleen	0.02 RPM	67.21 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3809 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3809 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3809 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
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,
Equus caballus	ENSECAG00000022693	1 retrocopy	retro_ecab_650,
Echinops telfairi	ENSETEG00000015624	3 retrocopies	retro_etel_1263, retro_etel_282, retro_etel_517,
Homo sapiens	ENSG00000122545	2 retrocopies	retro_hsap_3810, retro_hsap_4202,
Gorilla gorilla	ENSGGOG00000001175	1 retrocopy	retro_ggor_2816,
Monodelphis domestica	ENSMODG00000021167	1 retrocopy	retro_mdom_1672,
Nomascus leucogenys	ENSNLEG00000001673	1 retrocopy	retro_nleu_2152,
Otolemur garnettii	ENSOGAG00000006015	1 retrocopy	retro_ogar_1193,
Pongo abelii	ENSPPYG00000017639	1 retrocopy	retro_pabe_3438,
Pan troglodytes	ENSPTRG00000019080	2 retrocopies	retro_ptro_2585, retro_ptro_2853,
Rattus norvegicus	ENSRNOG00000006545	9 retrocopies	retro_rnor_1424, retro_rnor_1425, retro_rnor_1426, retro_rnor_1427, retro_rnor_1428, retro_rnor_1431, retro_rnor_1445, retro_rnor_1446, retro_rnor_821,
Sarcophilus harrisii	ENSSHAG00000003788	1 retrocopy	retro_shar_258,
Ictidomys tridecemlineatus	ENSSTOG00000021378	3 retrocopies	retro_itri_1332, retro_itri_1736, retro_itri_1771,
Tursiops truncatus	ENSTTRG00000016197	1 retrocopy	retro_ttru_329,