RetrogeneDB ID: retro_cjac_4137

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:7773749..7775035(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000000925
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CCNB1
• Ensembl ID: ENSCJAG00000016075
• Aliases: None
• Description: None

Sequence

>retro_cjac_4137
ATGGCGCTCCGAGTCACCAGGAACTCGAAAATTAATGCTGAAAATACGACGAAGATCAGTATGGCAGGCGCAAAGCGCGT
GCCTATGGCCCCTGCTGCAACCTCCAAGCCCGGACTGAGGCCAAGAACAGCTCTTGGGGACACTGGTAACAAAGTCAGTG
AACAGCTATAGGCCAAAATGCCTATGAAAAGGAGGGAAAACCTTCAGCTACTGGAAAAGTTATTGCTAAAAAACTACCAA
AACCTCTGGAAAAGGTACCTATGCTGGGGCCAGTGCCGGTGTCCCAGCCAGTGCCAGAGCCAGAACCTGAGCCTGTTAAA
AAAGAAAAACTTTCGCCTGAGCCTATTTTGGTTGACACTCCCTCCCTAAGCCCAATGGAAACATCTGGATGTGCCCCTGC
AGAAGAAGACCTATGTCAGGCTTTCTCTGATGTAATTCTTGCAGTAAATTATGTGGATGCAGAAGATGGAGTGGATCCAA
ACCTTTGTAGTGAATATGTGAAAGATATTTATGCTTATCTGAGACAACTTGAGGAAGAGCAAGCAGTCAGACCGAAATAC
CTACTGGGTCGGGAAGTCACTGGAAACATGAGAGCCATCCTAATTGACTGGCTAGTACAGGTCCAGATGAAATTCAGGTT
GTTGCAGGAGACCATGTACATGACTGTCTCCATTATTGATCGGTTCATGCAGAATAATTGTGTGCCCAAGAAGATGCTGC
AACTGGTTGGTGTCACTGCCATGTTTATTGCCAGCAAATATGAAGAAATGTACCCTCCAGAAATTGGTGACTTTGCTTTT
GTGACTGACAACACTTACACCAAGCCCCAGATCAGACAGATGGAAATGAAGATTCTAAGAGCTTTAAACTTTGGTCTGGG
TCGGCCTCTACCTTTGCACTTCCTTCGGAGAGCATCTAAGATTGGAGAGGCTGATGTTGACCAACATACTTTGGCCAAAT
ACCTGATGGAACTAACTATGTTGGACTATGATATGGTGTACTTTCCTCCTTCTCAAATTGCAGCAGGAGCTTTTTGCTTA
GCACTGAAAATTCTGGATGATGGTGAATGGACACCAACTCTACAGCATTACCTGTCATACACTGAAGAATCCCTTCTTCC
AGTTATGCAGCACCTGGCTAAGAATATAGTCATGGTAAATCAAGGGCTTACAAAGCACATGACTATCAAGAACAAGTATG
CTACGTCGAAACATGCTAAGATCAGCACTCTACCACAGCTGAATTCTGCACTAGTTCAAGATTTAGCCAAGGCTGTGGCA
AAGGTG

Alignment

ORF - retro_cjac_4137 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.91 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALRVTRNSKINAENTTKISMAGAKRVPMAPAATSKPGLRPRTALGDIGNKVSEQLQTKMPMK-KEGKPS
          MALRVTRNSKINAENTTKISMAGAKRVPMAPAATSKPGLRPRTALGD.GNKVSEQL..KMPMK.KEGKPS
Retrocopy MALRVTRNSKINAENTTKISMAGAKRVPMAPAATSKPGLRPRTALGDTGNKVSEQL*AKMPMK<KEGKPS

Parental  ATGKVIAKKLPKPLEKVPMLGPVPVSQPVPEPEPEPVKEEKLSPEPILVDTPSLSPMETSGCAPAEEDLC
          ATGKVIAKKLPKPLEKVPMLGPVPVSQPVPEPEPEPVK.EKLSPEPILVDTPSLSPMETSGCAPAEEDLC
Retrocopy ATGKVIAKKLPKPLEKVPMLGPVPVSQPVPEPEPEPVKKEKLSPEPILVDTPSLSPMETSGCAPAEEDLC

Parental  QAFSDVILAVNDVDAEDGVDPNLCSEYVKDIYAYLRQLEEEQAVRPKYLLGREVTGNMRAILIDWLVQVQ
          QAFSDVILAVN.VDAEDGVDPNLCSEYVKDIYAYLRQLEEEQAVRPKYLLGREVTGNMRAILIDWLVQVQ
Retrocopy QAFSDVILAVNYVDAEDGVDPNLCSEYVKDIYAYLRQLEEEQAVRPKYLLGREVTGNMRAILIDWLVQVQ

Parental  MKFRLLQETMYMTVSIIDRFMQNNCVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAFVTDNTYTKHQIR
          MKFRLLQETMYMTVSIIDRFMQNNCVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAFVTDNTYTK.QIR
Retrocopy MKFRLLQETMYMTVSIIDRFMQNNCVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAFVTDNTYTKPQIR

Parental  QMEMKILRALNFGLGRPLPLHFLRRASKIGEADVDQHTLAKYLMELTMLDYDMVHFPPSQIAAGAFCLAL
          QMEMKILRALNFGLGRPLPLHFLRRASKIGEADVDQHTLAKYLMELTMLDYDMV.FPPSQIAAGAFCLAL
Retrocopy QMEMKILRALNFGLGRPLPLHFLRRASKIGEADVDQHTLAKYLMELTMLDYDMVYFPPSQIAAGAFCLAL

Parental  KILDDGEWTPTLQHYLSYTEESLLPVMQHLAKNIVMVNQGLTKHMTIKNKYATSKHAKISTLAQLNSALV
          KILDDGEWTPTLQHYLSYTEESLLPVMQHLAKNIVMVNQGLTKHMTIKNKYATSKHAKISTL.QLNSALV
Retrocopy KILDDGEWTPTLQHYLSYTEESLLPVMQHLAKNIVMVNQGLTKHMTIKNKYATSKHAKISTLPQLNSALV

Parental  QDLAKAVAKV
          QDLAKAVAKV
Retrocopy QDLAKAVAKV

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	0.22 RPM	16.80 RPM
SRP051959_heart	0.14 RPM	1.35 RPM
SRP051959_kidney	0.33 RPM	1.35 RPM
SRP051959_liver	0.35 RPM	0.80 RPM
SRP051959_lung	0.34 RPM	2.96 RPM
SRP051959_lymph_node	0.02 RPM	4.57 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.66 RPM
SRP051959_spleen	0.23 RPM	4.89 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4137 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4137 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4137 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014239	2 retrocopies	retro_btau_1317, retro_btau_600,
Canis familiaris	ENSCAFG00000007705	1 retrocopy	retro_cfam_213,
Callithrix jacchus	ENSCJAG00000001593	1 retrocopy	retro_cjac_3884,
Callithrix jacchus	ENSCJAG00000001857	2 retrocopies	retro_cjac_3786, retro_cjac_3996,
Callithrix jacchus	ENSCJAG00000016075	1 retrocopy	retro_cjac_4137 ,
Cavia porcellus	ENSCPOG00000014629	1 retrocopy	retro_cpor_13,
Erinaceus europaeus	ENSEEUG00000005724	2 retrocopies	retro_eeur_386, retro_eeur_548,
Felis catus	ENSFCAG00000001572	1 retrocopy	retro_fcat_840,
Mustela putorius furo	ENSMPUG00000014648	1 retrocopy	retro_mputfur_58,
Mus musculus	ENSMUSG00000041431	5 retrocopies	retro_mmus_1170, retro_mmus_1550, retro_mmus_2508, retro_mmus_2615, retro_mmus_3023,
Procavia capensis	ENSPCAG00000002451	1 retrocopy	retro_pcap_176,
Rattus norvegicus	ENSRNOG00000018635	2 retrocopies	retro_rnor_568, retro_rnor_814,
Sarcophilus harrisii	ENSSHAG00000007685	1 retrocopy	retro_shar_290,
Tupaia belangeri	ENSTBEG00000011817	4 retrocopies	retro_tbel_1185, retro_tbel_3200, retro_tbel_4185, retro_tbel_4531,
Tarsius syrichta	ENSTSYG00000008928	1 retrocopy	retro_tsyr_232,