RetrogeneDB ID: retro_cjac_1259

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:14999516..15000794(-)
• Located in intron of: ENSCJAG00000013507

Retrocopy information

• Ensembl ID: ENSCJAG00000007762
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_1259
GAGGAGAGTATTTCAGACTTCAAGTATACAGCAGCTCAATGGAAGAACCTTGAAAGCTATGTGGGATTTGCCAATCTCCC
AAATCAAGTATATAGAAAATCAGTGAAGAGAGGTTTTGAATTCACGCTTATGGTAGTGGGCGAATCTGGATTGGGAAAGT
TGACATTAATCAACTCATTGTTCCTCACAGATCTGTATTCTCCAGAGTATCCAGGTCCTTCTCATAGAATTAAAAAGACT
GTACAGGTGGAACAATCCAACGTTTTAATCAAAGATGGTGGTGTTCAGTTGCTGCTCACAATACTTGATACCCCAGGATT
TGGAGATGCAGTGGATACTAGTAATTGCTGGCAGCCTGTTATCGACTACATTGATAGTAAATTTGAGGACTACCTAAATG
CAGAATCTCGAGTGAACAGACGCCAGATGCCTGATAATAGGGTGCAGTGTTGTTTATACTTCATTGCTCCTTCAGGACAT
GGACTTAAACCATTGGATATTGAGTTTATGAAGCGTTCGCATGAAAAAGTGAATATCATCCCACTTACTGCCAAAGCAGA
CACACTCACATAGAGGAATGCCAACAGTTTAAAAAACAGATAATGAAAGAAATCCAAGAACATAAAATTAAAATACGTGA
ATTTCCAGAAACAGATGATGAAGAAGAAAATAAACTTGTTAAAAAGATAAAGGACCGTTTACCTCTTGCTGTGGTCAGTA
GTAATACTATCATTGAAGTTAATGGCAAAAGGGTCAGAGGAAGGCAGTATCCTTGGGGTGTTGCTGAAGTTGAAAATGGT
GAACACTGTGATTTTACAATTCTAAGAAATATGTTGATAAGAACACACATGCAGGACCTGAAAGATGTTACTAATAATGT
TCACTATGAGAACTACAGAAGCAGAAAACTGGCAGCTGTGACTTATAGTGGAGTTGATAACAACAAGAATAAGGGCAGCT
GACTCAGAGCCCCTGGCACAGATGAAAGAAGAAAGAAGGGAGCGTGTAGCTAAAATGAAGAAGATGGAGATGGAGATGGA
GCCGTTGTTTGAGATGAAGGTCAAAGAAAAAGTTCAAAAACTGAAGGACTCTGAAGCTGAGCTCCAGCGGCGCAAGGAGC
AGATGAAAAAGAATTTGGAAGCACAGCACAAAGAATTAGAGGAAAAACGTCATCAGTTTGAGGATGAAAAAGCAAACTGG
GAAGCTCAACAGCGTATTTTAGAACAACAGAACTCTTCAAGAACCTTGGAAAAGAACAAGAAGAAAGGGAAGATCTTT

Alignment

ORF - retro_cjac_1259 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.7 %
• Parental protein coverage: 97.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ERSVNSSTMVCQQQKNLEGYVGFANLPNQVYRKSVKRGFEFTLMVVGESGLGKSTLINSLFLTDLYSPEY
          E.S.........Q.KNLE.YVGFANLPNQVYRKSVKRGFEFTLMVVGESGLGK.TLINSLFLTDLYSPEY
Retrocopy EESISDFKYTAAQWKNLESYVGFANLPNQVYRKSVKRGFEFTLMVVGESGLGKLTLINSLFLTDLYSPEY

Parental  PGPSHRIKKTVQVEQSKVLIKEGGVQLLLTIVDTPGFGDAVDNSNCWQPVIDYIDSKFEDYLNAESRVNR
          PGPSHRIKKTVQVEQS.VLIK.GGVQLLLTI.DTPGFGDAVD.SNCWQPVIDYIDSKFEDYLNAESRVNR
Retrocopy PGPSHRIKKTVQVEQSNVLIKDGGVQLLLTILDTPGFGDAVDTSNCWQPVIDYIDSKFEDYLNAESRVNR

Parental  RQMPDNRVQCCLYFIAPSGHGLKPLDIEFMKRLHEKVNIIPLIAKADTLT-PEECQQFKKQIMKEIQEHK
          RQMPDNRVQCCLYFIAPSGHGLKPLDIEFMKR.HEKVNIIPL.AKADTLT..EECQQFKKQIMKEIQEHK
Retrocopy RQMPDNRVQCCLYFIAPSGHGLKPLDIEFMKRSHEKVNIIPLTAKADTLT<IEECQQFKKQIMKEIQEHK

Parental  IKIYEFPETDDEEENKLVKKIKDRLPLAVVGSNTIIEVNGKRVRGRQYPWGVAEVENGEHCDFTILRNML
          IKI.EFPETDDEEENKLVKKIKDRLPLAVV.SNTIIEVNGKRVRGRQYPWGVAEVENGEHCDFTILRNML
Retrocopy IKIREFPETDDEEENKLVKKIKDRLPLAVVSSNTIIEVNGKRVRGRQYPWGVAEVENGEHCDFTILRNML

Parental  IRTHMQDLKDVTNNVHYENYRSRKLAAVTYNGVDNNKNK-GQLTKS-PLAQMEEERREHVAKMKKMEMEM
          IRTHMQDLKDVTNNVHYENYRSRKLAAVTY.GVDNNKNK.GQLT.S.PLAQM.EERRE.VAKMK......
Retrocopy IRTHMQDLKDVTNNVHYENYRSRKLAAVTYSGVDNNKNK<GQLTQS<PLAQMKEERRERVAKMKXXXXXX

Parental  EQVFEMKVKEKVQKLKDSEAELQRRHEQMKKNLEAQHKELEEKRRQFEDEKANWEAQQRILEQQNSSRTL
          ...FEMKVKEKVQKLKDSEAELQRR.EQMKKNLEAQHKELEEKR.QFEDEKANWEAQQRILEQQNSSRTL
Retrocopy XPLFEMKVKEKVQKLKDSEAELQRRKEQMKKNLEAQHKELEEKRHQFEDEKANWEAQQRILEQQNSSRTL

Parental  EKNKKKGKIF
          EKNKKKGKIF
Retrocopy EKNKKKGKIF

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	0.04 RPM	43.27 RPM
SRP051959_heart	0.16 RPM	72.07 RPM
SRP051959_kidney	0.04 RPM	54.07 RPM
SRP051959_liver	0.04 RPM	31.43 RPM
SRP051959_lung	0.13 RPM	78.86 RPM
SRP051959_lymph_node	0.05 RPM	68.10 RPM
SRP051959_skeletal_muscle	0.04 RPM	38.63 RPM
SRP051959_spleen	0.08 RPM	67.21 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1259 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1259 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1259 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,