RetrogeneDB ID: retro_cjac_923

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:72029511..72030393(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000021964
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPP1CA
• Ensembl ID: ENSCJAG00000000983
• Aliases: None
• Description: protein phosphatase 1, catalytic subunit, alpha isozyme [Source:HGNC Symbol;Acc:9281]

Sequence

>retro_cjac_923
ATGTCCGACAGCGAGAAGCTCAACCTGGACTCCATCATTGGGCGCCTGCTGGAAGTGCAGGGCTCGCAGCCTGGCAAGAT
TGTACAGCTGACTGAGAACGAGATTCGCGGTCTGTGCCTGAAATCCAGGGAGATTTTCCTGAGCCAGCCCATTCTTCTGG
ATCTGGAGGCACCCCTCAAGATCTGCGGTGACATCCACGGCCAGTACTACGACCTTCTGCGACTATTTGACTATGGGGGC
TTCCCTCCGGAGAGCAACTACCTCTTTCTGGGGGACTATGTGGACAGGGGCAAGCAGTCCTTGGAGACCATCTGCCTGCT
GCTGGCCTACAAGATCAAGTACCCCCAGAACTTCTTCCTGCTCCGTGGGAACCACGAGTGTGCCAGCATCAACCGCATCT
ATGGTTTCTACGATGAGTGCAAGAGACGCTACAACATCAAACTGTGGAAAACCTTCACTGACTGCTTTAACTGCCTGCCC
ATCGTAGCCATCGTGGATGAAAAGATCTTCTGCTGCCACGGAGGCTTGTCCCCAGACCTGCAATCCATGGAGCAGATCCG
GCGTATCATGAGGCCCACAGACGTGCCTGATCAGGGCCTGCTGTGTGACCTGCTGTGGTCTGACCCTGACAAGGACGTGC
AAGGCTGGGGCGAGAACGACCGTGGCGTCTCTTTTACCTTTGGAGCCGAGGTGGTGGCCAAGTTCCTGCACAAGCATGAC
TTGGACCTCATCTGCCGGGCGCACCAGGTGGTAGAAGATGGCTATGAGTTCTTTGCCAAGCGGCAGCTGGTGACACTTTT
CTCCGCTCCCAACTACTGTGGCGAGTTTGACAATGCTGGTGCCATGATGAGCGTGGACGAGACCCTCATGTGCTCCTTCC
AG

Alignment

ORF - retro_cjac_923 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.96 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSDSEKLNLDSIIGRLLEVQGSRPGKNVQLTENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYY
          MSDSEKLNLDSIIGRLLEVQGS.PGK.VQLTENEIRGLCLKSREIFLSQPILL.LEAPLKICGDIHGQYY
Retrocopy MSDSEKLNLDSIIGRLLEVQGSQPGKIVQLTENEIRGLCLKSREIFLSQPILLDLEAPLKICGDIHGQYY

Parental  DLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDEC
          DLLRLF.YGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYP.NFFLLRGNHECASINRIYGFYDEC
Retrocopy DLLRLFDYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPQNFFLLRGNHECASINRIYGFYDEC

Parental  KRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPD
          KRRYNIKLWKTFTDCFNCLPI.AIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPD
Retrocopy KRRYNIKLWKTFTDCFNCLPIVAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPD

Parental  KDVQGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAG
          KDVQGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAG
Retrocopy KDVQGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAG

Parental  AMMSVDETLMCSFQ
          AMMSVDETLMCSFQ
Retrocopy AMMSVDETLMCSFQ

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	4.22 RPM	29.49 RPM
SRP051959_heart	2.32 RPM	15.30 RPM
SRP051959_kidney	4.26 RPM	24.78 RPM
SRP051959_liver	3.62 RPM	26.38 RPM
SRP051959_lung	4.38 RPM	20.16 RPM
SRP051959_lymph_node	3.61 RPM	27.88 RPM
SRP051959_skeletal_muscle	3.36 RPM	23.24 RPM
SRP051959_spleen	3.19 RPM	21.64 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_923 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_923 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_923 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000004542	1 retrocopy	retro_cint_3,
Callithrix jacchus	ENSCJAG00000000983	1 retrocopy	retro_cjac_923 ,
Callithrix jacchus	ENSCJAG00000009147	7 retrocopies	retro_cjac_1062, retro_cjac_1165, retro_cjac_1408, retro_cjac_2304, retro_cjac_2535, retro_cjac_3288, retro_cjac_822,
Dasypus novemcinctus	ENSDNOG00000007986	3 retrocopies	retro_dnov_2565, retro_dnov_525, retro_dnov_872,
Drosophila melanogaster	FBgn0003134	5 retrocopies	retro_dmel_21, retro_dmel_37, retro_dmel_42, retro_dmel_48, retro_dmel_81,