RetrogeneDB ID: retro_cjac_915

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:59599339..59600342(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THUMPD1
• Ensembl ID: ENSCJAG00000009499
• Aliases: None
• Description: None

Sequence

>retro_cjac_915
AAGGCAAGGCTCAGTATGTGTTGGCCAAGTGGGCGCTGCGATACCGGCGGGCCCTGTCAGCTAGAGCCCAGGCTACAGGG
CATCCTCATCACCTGCAACATGAACAAGCGCAAGTGCGTGGAGGAGGCCTACAGTTTGCTCAACAAATACAGCGACGACA
TGTATGGGCCAGAAAAGCTTACAGACAAGGATCAGCACCCCTCTGGAAGTGAGGGAGAAGATGATGATGTGGAGGCTGCC
TTGAAGAAAGAAGTTGGTGATATTAAGGTATCTACAGAGATGAGGCTAAGAAGATTCCAGTCAGTGGAAAGTGGAGCAAA
TAACGTCATCTTCATCAGGACACTTGGGATAGAACCTGAGAAATTGGTGCATCATATTCTTCAGGATATGTACAAAACCA
AGAAGAAGAAGACTTGAGTTATTCTACGAATGTTACCCATCTCAGGCACATGCAAAGCTTTTTTAGAAGATATGAAAAAA
CATACAGAAACATTTTTGGAACCCTGGTTTAAAGCTCCGAACAAAGGGACAGTTCAGATTGTGTACCAATCTCGAAATAA
TAGTCACATGAATAGAGAAGAAGTTATCAGAGAATGGGCAGGAATAGTGGGCACCTTCAATTCAGAAAATAAAGTGAATC
TCACCAATCCACAGTACACGGTGGTAGTAGAAATCATCAAAGCTGTCTGTTGCCTGAGTGTTGTGAAAGATTGCATGTTG
TTGAGAAAATACAATCTCCAGGAGGTAGTGAAGAGCCCTAAGGATCCATCACAGCTTAACTCAAAGCAGGGAAATGGGAA
AGAAACTAAATTGGAAGCTGCTGACATCAGATCAAAACAACATAGCAGAAGGAAAAAATAACCAGCAGGTACCAGAGAAT
ACTGAGGAGCTGGGGCAGACAAAACCAACGTCTAATCCGCAGGTGGTGAATGAGGGAGGAGGCAAACCTGAACTTGCAAG
TCAAGCCACAGAAGGACCCAAATCAAATGAAAATGACCTCTCA

Alignment

ORF - retro_cjac_915 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.31 %
• Parental protein coverage: 94.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KAQYVLAKRARRCDAGGPHQLEPGLQGILITCNMNERKCVEEAYSLLNEYGDDMYGPEKLTDKDQQPSGS
          KA.........RCD.GGP.QLEP.LQGILITCNMN.RKCVEEAYSLLN.Y.DDMYGPEKLTDKDQ.PSGS
Retrocopy KARLSMCWPSGRCDTGGPCQLEPRLQGILITCNMNKRKCVEEAYSLLNKYSDDMYGPEKLTDKDQHPSGS

Parental  EGEDDDVEAALKKEVGDIKASTEMRLRRFQSVESGANNVVFIRTLGIEPEKLVHHILQDMYKTKKKKTRV
          EGEDDDVEAALKKEVGDIK.STEMRLRRFQSVESGANNV.FIRTLGIEPEKLVHHILQDMYKTKKKKT.V
Retrocopy EGEDDDVEAALKKEVGDIKVSTEMRLRRFQSVESGANNVIFIRTLGIEPEKLVHHILQDMYKTKKKKT*V

Parental  ILRMLPISGTCKAFLEDMKKYAETFLEPWFKAPNKGTFQIVYKSRNNSHMNREEVIRELAGIVGTLNSEN
          ILRMLPISGTCKAFLEDMKK..ETFLEPWFKAPNKGT.QIVY.SRNNSHMNREEVIRE.AGIVGT.NSEN
Retrocopy ILRMLPISGTCKAFLEDMKKHTETFLEPWFKAPNKGTVQIVYQSRNNSHMNREEVIREWAGIVGTFNSEN

Parental  KVNLTNPQYTVVVEIIKAVCCLSVVKDYMLFRKYNLQEVVKSPKDPSQLISKQGNGTETKLESADKSDQN
          KVNLTNPQYTVVVEIIKAVCCLSVVKD.ML.RKYNLQEVVKSPKDPSQL.SKQGNG.ETKLE.AD.....
Retrocopy KVNLTNPQYTVVVEIIKAVCCLSVVKDCMLLRKYNLQEVVKSPKDPSQLNSKQGNGKETKLEAADIRSKQ

Parental  NIAEGK-NNQQVPQNTDELGQTKPTSNPQVVNEGGGKPELASQATEGSKSNENDLS
          .....K.N.Q.VP.NT.ELGQTKPTSNPQVVNEGGGKPELASQATEG.KSNENDLS
Retrocopy HSRRKK>NQQ-VPENTEELGQTKPTSNPQVVNEGGGKPELASQATEGPKSNENDLS

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	0.18 RPM	15.49 RPM
SRP051959_heart	0.39 RPM	16.12 RPM
SRP051959_kidney	0.47 RPM	47.66 RPM
SRP051959_liver	0.11 RPM	17.11 RPM
SRP051959_lung	0.26 RPM	18.51 RPM
SRP051959_lymph_node	0.43 RPM	18.22 RPM
SRP051959_skeletal_muscle	0.11 RPM	11.66 RPM
SRP051959_spleen	0.57 RPM	20.61 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_915 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_915 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_915 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009499	1 retrocopy	retro_cjac_915 ,
Cavia porcellus	ENSCPOG00000008919	1 retrocopy	retro_cpor_71,
Felis catus	ENSFCAG00000015158	1 retrocopy	retro_fcat_195,
Homo sapiens	ENSG00000066654	1 retrocopy	retro_hsap_2521,
Gorilla gorilla	ENSGGOG00000005231	1 retrocopy	retro_ggor_1573,
Macaca mulatta	ENSMMUG00000004225	1 retrocopy	retro_mmul_1599,
Monodelphis domestica	ENSMODG00000006971	1 retrocopy	retro_mdom_54,
Nomascus leucogenys	ENSNLEG00000012369	1 retrocopy	retro_nleu_1443,
Pan troglodytes	ENSPTRG00000007848	1 retrocopy	retro_ptro_1466,