RetrogeneDB ID: retro_cjac_4035

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL290141.1:6687..8346(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000004026
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GK
• Ensembl ID: ENSCJAG00000007633
• Aliases: None
• Description: None

Sequence

>retro_cjac_4035
ATGGCAGCCTCAAATAAGTCAGTTTTGGGGCCATTGGTAGGGGCGGTGGACCAGGGCACCAGTTCCACACGCTTTTTGGT
TTTCAGTTCAAAAACAGCTGAACTGCTCAGTCATCATCAAGTGGAAATAAAACAAGAGTTTCCCAGAGAAGGATGGGTGG
AACAAGACCCGAAGGAAATTCTGCATTCTGTCTATGAGTGTATAGAGAAAACATGTGAGAAACTCGGACAGCTCAATATT
GATATTTCCAACATCAAAGCTATTGGCGTCAGCAACCAGAGAGAAACCACTGTAGTCTGGGACAAGTTAACTGGAGAGCC
TCTCTACAATGCTGTGGTGTGGCTTGACCTAAGAACCCAGTCTACCGTTGAGAGTCTTGGTAAAAGAATTCCAAGAAGTA
ACAACTTTGTCAAGTCCAAGACAGGCCTTCCACTTAGCACTTACTTCAGCGCCGTGAAACTTCGTTGGCTCCTTGACAAT
GTGAGAAAAGTTCGAAAGGCTGTTGAAGAAAAACGAGCGCTTTTTGGAACTATTGATTCATGGCTTATTTGGAGTTTGAC
GGGAGGAGTCAATGGAGGGGTCCACAATACGGATGTAACAAATGCAAGCAGGACTATGCTTTTCAACATTCATTCTTTGG
AATGGGATAAACAGCTCTGTGAATTTTTTGGAATTCCAATGGAAATTCTTCCAAATGTCCGGAGTTCTTCTGAGATCTAT
GGCCTAATGAAAGCTGGGGCCCTGGAAGGTGTGCCAATATCTGGGTGTTTAGGGGACCAGTCTGCTGCATTGGTGGGACA
AATGTGCTTCCAGAATGGACAAGCCAAAAATACGTATGGAACGGGATGTTTCTTACTATGTAATACAGGCCGTACATGTG
TATTTTCTGATCATGGTCTTCTCACCACAGTGGCTTACAAACTTGGCAGAGACAAACCGGTATATTATGCATTGGAAGGT
TCTGTAGCTATAGCTGGTGCTGTTATTCGCTGGCTAAGAGACAATCTTGGAATTATAAAGACCTCAGAAGAAATTGAAAA
ACTTGCTAAAGAAGTAGGTACTTCTTATGGCTGCTACTTTGTCCCAGCATTTTCGGGGTTATATGCACCTTATTGGGAGC
CCAGTGCAAGGGGGATAATCTGTGGACTCACTCAGTTCACCAATAAATGCCATATTGCTTTTGCTGCATTAGAAGCTGTT
TGTTTCCAAACTCGAGAGATTTTGGATGCCATGAATCGAGACTGTGGAATTCCACTCAGTCATTTGCAGGTAGATGGAGG
AATGACCAGCAACAAAATCCTTATGCAGCTACAAGCAGACATTCTGTATATTCCAGTAGTTAAGTCCCTGATGCCTGAAA
CCACTGCACTGGGTGCCGCCATGGCAGCAGGGGCTGCGGAAGGAGTCGGCGTATGGAGTCTCGAACCTGAGGATTTGTCT
ACCATCACGATGGAGCGGTTTGAACCTCAGATTAATGCTGAGGAAAGTGAAATTCGTTATTCTACATGGAAGAAAGCTGT
GATGAAGTCAATGGGTTGGGTTACAACTCAGTCTCCAGAAAGTGGTGACCCTAGTATCTTCTGCAGTGTGTCCTTGGGCT
TTTTTATAGTGAGTAGCATGGTAATGTTAATTGGAGCAAGGTACATCTCAGGTATCCCA

Alignment

ORF - retro_cjac_4035 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.75 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAASKKAVLGPLVGAVDQGTSSTRFLVFNSKTAELLSHHQVEIKQEFPREGWVEQDPKEILHSVYECIEK
          MAAS.K.VLGPLVGAVDQGTSSTRFLVF.SKTAELLSHHQVEIKQEFPREGWVEQDPKEILHSVYECIEK
Retrocopy MAASNKSVLGPLVGAVDQGTSSTRFLVFSSKTAELLSHHQVEIKQEFPREGWVEQDPKEILHSVYECIEK

Parental  TCEKLGQLNIDISNIKAIGVSNQRETTVVWDKLTGEPLYNAVVWLDLRTQSTVESLSKRIPGNNNFVKSK
          TCEKLGQLNIDISNIKAIGVSNQRETTVVWDKLTGEPLYNAVVWLDLRTQSTVESL.KRIP..NNFVKSK
Retrocopy TCEKLGQLNIDISNIKAIGVSNQRETTVVWDKLTGEPLYNAVVWLDLRTQSTVESLGKRIPRSNNFVKSK

Parental  TGLPLSTYFSAVKLRWLLDNVRKVQKAVEEKRALFGTIDSWLIWSLTGGVNGGVHCTDVTNASRTMLFNI
          TGLPLSTYFSAVKLRWLLDNVRKV.KAVEEKRALFGTIDSWLIWSLTGGVNGGVH.TDVTNASRTMLFNI
Retrocopy TGLPLSTYFSAVKLRWLLDNVRKVRKAVEEKRALFGTIDSWLIWSLTGGVNGGVHNTDVTNASRTMLFNI

Parental  HSLEWDKQLCEFFGIPMEILPNVRSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQNGQAKNTYG
          HSLEWDKQLCEFFGIPMEILPNVRSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQNGQAKNTYG
Retrocopy HSLEWDKQLCEFFGIPMEILPNVRSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQNGQAKNTYG

Parental  TGCFLLCNTGHKCVFSDHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVIRWLRDNLGIIESSEEIEKLAK
          TGCFLLCNTG..CVFSDHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVIRWLRDNLGII..SEEIEKLAK
Retrocopy TGCFLLCNTGRTCVFSDHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVIRWLRDNLGIIKTSEEIEKLAK

Parental  EVGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNKCHIAFAALEAVCFQTREILDAMNRDCGIPLS
          EVGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNKCHIAFAALEAVCFQTREILDAMNRDCGIPLS
Retrocopy EVGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNKCHIAFAALEAVCFQTREILDAMNRDCGIPLS

Parental  HLQVDGGMTSNKILMQLQADILYIPVVKPSMPETTALGAAMAAGAAEGVGVWSLEPEDLSAVTMERFEPQ
          HLQVDGGMTSNKILMQLQADILYIPVVK..MPETTALGAAMAAGAAEGVGVWSLEPEDLS..TMERFEPQ
Retrocopy HLQVDGGMTSNKILMQLQADILYIPVVKSLMPETTALGAAMAAGAAEGVGVWSLEPEDLSTITMERFEPQ

Parental  INAEESEIRYSTWKKAVMKSMGWVTTQSPESGDPSIFCSLPLGFFIVSSMVMLIGARYISGIP
          INAEESEIRYSTWKKAVMKSMGWVTTQSPESGDPSIFCS..LGFFIVSSMVMLIGARYISGIP
Retrocopy INAEESEIRYSTWKKAVMKSMGWVTTQSPESGDPSIFCSVSLGFFIVSSMVMLIGARYISGIP

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	0.02 RPM	23.52 RPM
SRP051959_heart	0.05 RPM	6.44 RPM
SRP051959_kidney	0.04 RPM	47.17 RPM
SRP051959_liver	0.00 RPM	25.47 RPM
SRP051959_lung	0.02 RPM	14.61 RPM
SRP051959_lymph_node	0.00 RPM	4.09 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.92 RPM
SRP051959_spleen	0.00 RPM	8.76 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4035 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4035 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4035 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001924	1 retrocopy	retro_cjac_478,
Callithrix jacchus	ENSCJAG00000007633	3 retrocopies	retro_cjac_125, retro_cjac_3161, retro_cjac_4035 ,
Cavia porcellus	ENSCPOG00000003261	2 retrocopies	retro_cpor_11, retro_cpor_20,
Echinops telfairi	ENSETEG00000008279	2 retrocopies	retro_etel_2000, retro_etel_247,
Felis catus	ENSFCAG00000004264	1 retrocopy	retro_fcat_140,
Homo sapiens	ENSG00000198814	4 retrocopies	retro_hsap_3087, retro_hsap_3120, retro_hsap_4885, retro_hsap_70,
Loxodonta africana	ENSLAFG00000007632	1 retrocopy	retro_lafr_30,
Monodelphis domestica	ENSMODG00000002417	1 retrocopy	retro_mdom_234,
Mus musculus	ENSMUSG00000025059	2 retrocopies	retro_mmus_119, retro_mmus_97,
Nomascus leucogenys	ENSNLEG00000010102	2 retrocopies	retro_nleu_1650, retro_nleu_771,
Oryctolagus cuniculus	ENSOCUG00000013023	2 retrocopies	retro_ocun_2, retro_ocun_81,
Rattus norvegicus	ENSRNOG00000034116	2 retrocopies	retro_rnor_114, retro_rnor_34,
Sarcophilus harrisii	ENSSHAG00000006470	1 retrocopy	retro_shar_35,
Ictidomys tridecemlineatus	ENSSTOG00000008732	1 retrocopy	retro_itri_1436,
Tarsius syrichta	ENSTSYG00000008249	1 retrocopy	retro_tsyr_29,