RetrogeneDB ID: retro_cjac_1322

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:16163473..16164605(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000034720
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000005913
• Aliases: None
• Description: None

Sequence

>retro_cjac_1322
GTGGTGTGGGATTGGGTGTGGCAGCAGCCAGTACCGGACTTTGAGAGTGGCCACAAAAGTAATGTGTTCCAGGCCAAGTT
TCTTCTAATAGCGGTGATTCCACTCTGGCCATATGTGCCCGTGACAGGCAGGTTTGGGTAGCAGAACTGACTGCCACACA
GTGTTGCAAGAATATGAAATGTGCGGCCCAGCACAAGGGAGCGTCTCACAAGTTGGCTCTGGAACCAGACTCTCCCTGTA
TGTTCTTATCTGCAGGTAAAGATGCAGTTGTTTTCACCACTGACCTGAGACAAGACCGCCGAGCTTCGAAACTGGTGCTA
ACAAAAGAGAAAGAGAAGAAAGTGGGGCTGTATGCAATCTATGTGAATCCTGCCAATACCCACCAGTTTGCAGTGGGCGA
CGAGATCCGTTTGTAACGATTTATGACCAGAGGAAAACTGATAAGAATGAGAACAATGGAGTACTCAAAAGTTCTGCCCT
CATCACCTGGTGAACAGTGAGTCCAAAGCAAACACCGCCTGTCTTGTGTACAGCCACGATGGCACAGAGCTCCTATCAGG
TACAATGATGAACACATTTACCTCTTCAACTCCTCTCACAGTCATGGGGCCCAGTATGTTAAGAGATATAAGGGCCACAG
AAATAATGCCACAGTAAAAGGTGTCAATTTCTATGACCCCAAGAGTGAGTTTGTGGTTAGCAGTAGTGACTGTGGGCACA
TCTTCCTCTGGGAGAAATCATCCTGCCAGAGTAGTCAGTTCATGGAGGGGGACAAGGGAGGCATGGTAAACTGTCTTGAG
CCCCACCCTCACCTGCCTGTACTGGCAACTAGTGGCCTAGACCATGATGTGATCTGGCCACCCACAGCTGAAGATTCCAC
TGAGCTGACGAGGTTAAAAGATGTGATTAAGAAGAACAAGCAGGGGTGGGATGAAGATGGTTTGCACCACACTGACCTAT
TTGATAGTCACATGCTGTGCTTCCTCATGCATCACCTGAGACAGAGACGTCTCACCAGCACTGGCGAGAACCTGGGGTTG
GGGCCACAGACGCAGACTCTGATGAATCTCCCAGCTCCTCAGATACATCAGAGGAGGAGGAAGGCCCTAACCGAGTGCAG
TGCATGTCATCT

Alignment

ORF - retro_cjac_1322 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.97 %
• Parental protein coverage: 63.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VVWDWVRRQPVLDFESGHKSNVFQAKFL-PNSGDSTLAMCARDGQVRVAELSATQCCKNTKRVAQHKGAS
          VVWDWV..QPV.DFESGHKSNVFQAKFL..NSGDSTLA.CARD.QV.VAEL.ATQCCKN.K..AQHKGAS
Retrocopy VVWDWVWQQPVPDFESGHKSNVFQAKFL<SNSGDSTLAICARDRQVWVAELTATQCCKNMKCAAQHKGAS

Parental  HKLALEPDSPCTFLSAGEDAVVFTIDLRQDRPASKLVVTKEKEKKVGLYTIYVNPANTHQFAVGG-RDQF
          HKLALEPDSPC.FLSAG.DAVVFT.DLRQDR.ASKLV.TKEKEKKVGLY.IYVNPANTHQFAVG..RD.F
Retrocopy HKLALEPDSPCMFLSAGKDAVVFTTDLRQDRRASKLVLTKEKEKKVGLYAIYVNPANTHQFAVGD<RDPF

Parental  VRIYDQRKIDENENNGVLK-KFCPHHLVNSESKANITCLVYSHDGTELLAS-YNDEDIYLFNSSHSDGAQ
          V.IYDQRK.D.NENNGVLK.KFCPHHLVNSESKAN..CLVYSHDGTELL...YNDE.IYLFNSSHS.GAQ
Retrocopy VTIYDQRKTDKNENNGVLK<KFCPHHLVNSESKANTACLVYSHDGTELLSG<YNDEHIYLFNSSHSHGAQ

Parental  YVKRYKGHRNNATVKGVNFYGPKSEFVVSGSDCGHIFLWEKSSCQIIQFMEGDKGGVVNCLEPHPHLPVL
          YVKRYKGHRNNATVKGVNFY.PKSEFVVS.SDCGHIFLWEKSSCQ..QFMEGDKGG.VNCLEPHPHLPVL
Retrocopy YVKRYKGHRNNATVKGVNFYDPKSEFVVSSSDCGHIFLWEKSSCQSSQFMEGDKGGMVNCLEPHPHLPVL

Parental  ATSGLDHDVKIWAPTAEASTELTGLKDVIKKNKRDRDEESLHHTDLFDSHMLWFLMHHLRQRR-HHRRWR
          ATSGLDHDV.IW.PTAE.STELT.LKDVIKKNK...DE..LHHTDLFDSHML.FLMHHLRQRR..H..WR
Retrocopy ATSGLDHDV-IWPPTAEDSTELTRLKDVIKKNKQGWDEDGLHHTDLFDSHMLCFLMHHLRQRR<SHQHWR

Parental  EPGVGATDADSDESPSSSDTSDEEEGPDRVQCMPS
          EPGVGATDADSDESPSSSDTS.EEEGP.RVQCM.S
Retrocopy EPGVGATDADSDESPSSSDTSEEEEGPNRVQCMSS

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	3.11 RPM	24.05 RPM
SRP051959_heart	2.49 RPM	52.59 RPM
SRP051959_kidney	3.66 RPM	59.30 RPM
SRP051959_liver	1.71 RPM	51.21 RPM
SRP051959_lung	2.55 RPM	45.57 RPM
SRP051959_lymph_node	2.17 RPM	36.73 RPM
SRP051959_skeletal_muscle	2.18 RPM	84.19 RPM
SRP051959_spleen	1.95 RPM	41.87 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1322 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1322 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1322 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014293	1 retrocopy	retro_amel_47,
Bos taurus	ENSBTAG00000005796	1 retrocopy	retro_btau_1853,
Canis familiaris	ENSCAFG00000031010	1 retrocopy	retro_cfam_223,
Callithrix jacchus	ENSCJAG00000005913	1 retrocopy	retro_cjac_1322 ,
Echinops telfairi	ENSETEG00000012876	1 retrocopy	retro_etel_654,
Felis catus	ENSFCAG00000003925	1 retrocopy	retro_fcat_14,
Mustela putorius furo	ENSMPUG00000013949	1 retrocopy	retro_mputfur_173,
Mus musculus	ENSMUSG00000026554	1 retrocopy	retro_mmus_111,
Otolemur garnettii	ENSOGAG00000011349	1 retrocopy	retro_ogar_2113,
Pteropus vampyrus	ENSPVAG00000007982	1 retrocopy	retro_pvam_1356,
Sus scrofa	ENSSSCG00000006388	1 retrocopy	retro_sscr_88,
Tupaia belangeri	ENSTBEG00000001566	1 retrocopy	retro_tbel_3644,