RetrogeneDB ID: retro_cjac_766

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:20906114..20907191(-)
• Located in intron of: ENSCJAG00000002506

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPDL1
• Ensembl ID: ENSCJAG00000004745
• Aliases: None
• Description: spindle apparatus coiled-coil protein 1 [Source:HGNC Symbol;Acc:26010]

Sequence

>retro_cjac_766
GTGGAAGCAGATATAATTGCAAATCTTTCATGCAAGCTCAAAGAAGTTGAAGAAGAGAGACTAAAAGCTGCGCAGTACGG
TTTACAACTAGTAGAGAGTCAAAATGAATTATAGAATCAATTGGATAAATGTCGTAATGAAATGATGACCATGACTGAGA
GTTATGAACATGAAAAATATACCCTTCAAAGAGAAGTTGAACTCAAGAGTCGAATGTTAGAAAGTTTGAGCTCTGAATGT
GAAGTTATTAAACAACAAAAAATACACCTGGAGTAATTGGAAGAACAACTAAACAGAAGCCATGGGCAGGAAGTGAATGA
ACTAAAAACTAAGATAGAAAAATTGAAAGTGGAATTAGATGAAGCTAGGCTTAGTGAAAAACAGTTGAAGCACCAAATGG
ATCATCAGAAGGAACTCCTCTCTTGTAACTCAGAGGAACTGTGCATAATGTCTGGACGTGTGCAGGAAAGCATGTCTTCA
GAGATGCTGGCTCTTCAAATTGAGCTGACAGAAATGGAGAGTATGATGACCACCCTCAAAGAAGTGAATGAACTACAAAA
CAGACAAGAACAGCTAGAACTTATTACTAACCTAATGCATCAGGTAGACCAGCCTTTTAAAGAGGAAAAAGAGGAGCAAG
AAAAAGAAGCAGATTCTTACTATAATGCTCTAGAGAAAGCTCATGTAGCAAATGAAGATCTTCAGGTGCAGTTGGACCAG
GCAATCCAGCAAGCCTTGGATCCTAATAGTAAAGGCAACTCTTTGTTTGCAGAGGTAGAAGATCGAAGGGCAGCAATGGA
ATGTCAGCTTATCAGTATGAAAGTCAAGTATCAGTCACTAAGGAAGCAAAATGTATTTAACAGAGAGCAGATGCAGAGAA
TGAAGTTACAAATCGCCACATTGCTACAGATCAAAGGGTCTCAAACTGAATTTGAGCAGCAGGAACGGTTGCTTGCCATG
TTGGAGCAGAAGAATGGTGAAATAAAACATCTTTTAGGTGAAATTAGAAATCTGGAGAAAGTTAAGAATTTATATGAAAG
TATGGAATCTAAGCCTTCACTCCACTCTGGTACTCTG

Alignment

ORF - retro_cjac_766 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.06 %
• Parental protein coverage: 59.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEADIIANLRCKLKEAEEERLKAAQYGLQLVESQNELQNQLDKCRNEMMTMTESYEQEKYTLQREVELKS
          .EADIIANL.CKLKE.EEERLKAAQYGLQLVESQNEL.NQLDKCRNEMMTMTESYE.EKYTLQREVELKS
Retrocopy VEADIIANLSCKLKEVEEERLKAAQYGLQLVESQNEL*NQLDKCRNEMMTMTESYEHEKYTLQREVELKS

Parental  RMLESFSSECEVIKQQQKIHLEKLEQQLSRSHGQEVNELKTKIEKLKVELDEARLSEKQLKHQIDHQKEL
          RMLES.SSECEVIKQQ.KIHLE.LE.QL.RSHGQEVNELKTKIEKLKVELDEARLSEKQLKHQ.DHQKEL
Retrocopy RMLESLSSECEVIKQQ-KIHLE*LEEQLNRSHGQEVNELKTKIEKLKVELDEARLSEKQLKHQMDHQKEL

Parental  LSCKSEELRIMSGRVQESMSSEMLALQIELTEMESMKTTLTEEVNELQYRQEQLELLITNLMRQVDR-LK
          LSC.SEEL.IMSGRVQESMSSEMLALQIELTEMESM.TTL..EVNELQ.RQEQLEL.ITNLM.QVD...K
Retrocopy LSCNSEELCIMSGRVQESMSSEMLALQIELTEMESMMTTL-KEVNELQNRQEQLEL-ITNLMHQVDQPFK

Parental  EEKDEREKEAVSYYNALEKARVANQDLQVQLDQALQQALDSNSKGNSLFAEVEDRRAAMERQLITMKVKY
          EEK.E.EKEA.SYYNALEKA.VAN.DLQVQLDQA.QQALD.NSKGNSLFAEVEDRRAAME.QLI.MKVKY
Retrocopy EEKEEQEKEADSYYNALEKAHVANEDLQVQLDQAIQQALDPNSKGNSLFAEVEDRRAAMECQLISMKVKY

Parental  QSLKKQNVFNREQMQRMKLQIATLLQMKGSQTEFEQQERLLAMLEQKNGEIKHLLGEIRNLEKFKNLYES
          QSL.KQNVFNREQMQRMKLQIATLLQ.KGSQTEFEQQERLLAMLEQKNGEIKHLLGEIRNLEK.KNLYES
Retrocopy QSLRKQNVFNREQMQRMKLQIATLLQIKGSQTEFEQQERLLAMLEQKNGEIKHLLGEIRNLEKVKNLYES

Parental  MESKPSVHSGAL
          MESKPS.HSG.L
Retrocopy MESKPSLHSGTL

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	0.27 RPM	4.50 RPM
SRP051959_heart	0.14 RPM	3.42 RPM
SRP051959_kidney	0.16 RPM	2.11 RPM
SRP051959_liver	0.09 RPM	1.30 RPM
SRP051959_lung	0.31 RPM	3.56 RPM
SRP051959_lymph_node	0.46 RPM	3.88 RPM
SRP051959_skeletal_muscle	0.13 RPM	2.29 RPM
SRP051959_spleen	0.27 RPM	4.79 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_766 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_766 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_766 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013141	5 retrocopies	retro_chof_1356, retro_chof_1565, retro_chof_1882, retro_chof_198, retro_chof_2505,
Callithrix jacchus	ENSCJAG00000004745	1 retrocopy	retro_cjac_766 ,