RetrogeneDB ID: retro_cjac_4042

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:11276857..11278597(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAF5L
• Ensembl ID: ENSCJAG00000010986
• Aliases: None
• Description: None

Sequence

>retro_cjac_4042
CAGATTCAGATGGCAGTGTCCTGCTACCTCAAATGCCGGCAGTATGTGGACTCCGATGGTCCCCTGAAACAAGGACTGTG
GCTGTCACAGACTGCTGAAGAGATGGCGGCCAATCTGACGGTGCAATCAGAATCTGCTTGTGCCAACATAGTGTCTGCAG
CCCCTTGCCAGGCGGAACCCCAGCAATATGAAGTCCAGTTTGGATGACTGCAGAATTTTCTCACCGATTCTGATTCCCAG
CATAGCCATGAAGTGATGCCTCTCCTCTATCCTCTCTTTGTCTACCTCCATCTCAGCCTGGTCCAGAACAGTCCGAAGAG
CACAGTGGAAAGTTTTTACAGCCACTTCCATGGAATGTTTCTGCAGAACGCTAGCCAGAAGGATGTCATTGAGCAGCTAC
AGACCACTCAAACCATCCAGGACATCCTGTCTAACTTCAAGCTTCGAGCATTCCTAGATAACAAGTACGTGGTCCGTCTC
CAAGAAGACAGCTACAACTACCTTATCCGCTACCTCCGAAGTGACAATACTGCCCTGTGCAGAGTTCTCACCTTACGTAT
TCATCTTGACGTGCAGCCTGCCAAGAGAACATACTACCAGCTATATGCCAGTGGCAGCTCCTCCTGCAGTGAGAACAACA
GCTTGGAGCCCCCTGACATGCCCAGCCCTATTCTACAGAACGAGGCTACCCTGGAGGTCTTACAGGAGAGCATTAAGCGC
ATCAAAGATGGGCCTCCCTCCATCACTACCATCTGCTTCTATGCCTTCTATAACACAGAGCACCTGTTGAACACTGCAGA
AATCTCCCCCGATAGCAAACTACTTGCCACTGGGTTTGACAACTCCTGTATAAAGCTTTGGAGTTTACGATCCAAGAAGT
TAAAATCAGAGCCCCATCAAGTAGACGTGTCCCGCATCCATTTGGCTTGTGATATTCTGGAGGAGGAGGATGATGAGGAT
GATAATGCAGGCACAGAGATGAAGATACTGTGGGGACACTGCGGACTGGTATACAGCACGAGGTTCCTCGCGGACAGCTC
AGGGTTGCTCTCTTGTTCTGAAGACATGCCCATCAGATACTGGGATCTGGGGAGTTTCACCAACACTGTGTTGTACCAAG
GACATGCCTGTCCCGTGTGGGATCTGGGCATCAGTCCATATAGCCTGTACTTCGCCAGCGGGTCCCACGATTGCACCGCC
AGACTGTGGTCATTTGATCGGACATACCCGCTGAGGATATATGCAGGACACCTGGCAGATGTGGCCTGTGTCAAATTCCA
CCCTAATTCAAACTACTTAGCTACGGGCTCAACCAACAAGACCGTCTGGCTATGGAGCGCGCAGTAGGGGAACTTGGTGA
GGCTTTTCACAGGCCACCATGGCCCTGTGCTTTCTCTTGCCTTTTCTCCTAACAGTAAGTACTTGGCGTCTGCTGGCAAG
GACCAGCGGTTGAAGCTGTGGGACTTGGCCTCTGGGACCCTTTATAAAGAGCTGAGAGGCCACACAGACAATATCACCAG
CCTCACCTTCAGTCCAGACAGCGGCTTGATTGCCTCTGCCTCCATGGACAACTCGGTGCGCGTCTGGGACATCAGGAACA
GTTATTGCAGTGTACCTGCCTACGGCTCCTCCAGTGAGCTCGTGGGCCTGTACATCGGGCAGATGAGCAGCATCTTGAGC
ATGCAGTTCATGGCCTGTAACCTTCTGGTAACTTGAATTACACAAGAAAATCAGGAACAT

Alignment

ORF - retro_cjac_4042 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.78 %
• Parental protein coverage: 98.81 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QIQMAVSCYLKRRQYVDSDGPLKQGLRLSQTAEEMAANLTVQSESGCANIVSAAPCQAEPQQYEVQFGRL
          QIQMAVSCYLK.RQYVDSDGPLKQGL.LSQTAEEMAANLTVQSES.CANIVSAAPCQAEPQQYEVQFG.L
Retrocopy QIQMAVSCYLKCRQYVDSDGPLKQGLWLSQTAEEMAANLTVQSESACANIVSAAPCQAEPQQYEVQFG*L

Parental  RNFLTDSDSQHSHEVMPLLYPLFVYLHLNLVQNSPKSTVESFYSRFHGMFLQNASQKDVIEQLQTTQTIQ
          .NFLTDSDSQHSHEVMPLLYPLFVYLHL.LVQNSPKSTVESFYS.FHGMFLQNASQKDVIEQLQTTQTIQ
Retrocopy QNFLTDSDSQHSHEVMPLLYPLFVYLHLSLVQNSPKSTVESFYSHFHGMFLQNASQKDVIEQLQTTQTIQ

Parental  DILSNFKLRAFLDNKYVVRLQEDSYNYLIRYLQSDNNTALCRVLTLHIHLDVQPAKRTDYQLYASGSSSR
          DILSNFKLRAFLDNKYVVRLQEDSYNYLIRYL.SDN.TALCRVLTL.IHLDVQPAKRT.YQLYASGSSS.
Retrocopy DILSNFKLRAFLDNKYVVRLQEDSYNYLIRYLRSDN-TALCRVLTLRIHLDVQPAKRTYYQLYASGSSSC

Parental  SENNGLEPPDMPSPILQNEAALEVLQESIKRVKDGPPSLTTICFYAFYNTEQLLNTAEISPDSKLLAAGF
          SENN.LEPPDMPSPILQNEA.LEVLQESIKR.KDGPPS.TTICFYAFYNTE.LLNTAEISPDSKLLA.GF
Retrocopy SENNSLEPPDMPSPILQNEATLEVLQESIKRIKDGPPSITTICFYAFYNTEHLLNTAEISPDSKLLATGF

Parental  DNSCIKLWSLRSKKLKSEPHQVDVSRIHLACDILEEEDDEDDNAGTEMKILRGHCGPVYSTRFLADSSGL
          DNSCIKLWSLRSKKLKSEPHQVDVSRIHLACDILEEEDDEDDNAGTEMKIL.GHCG.VYSTRFLADSSGL
Retrocopy DNSCIKLWSLRSKKLKSEPHQVDVSRIHLACDILEEEDDEDDNAGTEMKILWGHCGLVYSTRFLADSSGL

Parental  LSCSEDMSIRYWDLGSFTNTVLYQGHAYPVWDLDISPYSLYFASGSHDRTARLWSFDRTYPLRIYAGHLA
          LSCSEDM.IRYWDLGSFTNTVLYQGHA.PVWDL.ISPYSLYFASGSHD.TARLWSFDRTYPLRIYAGHLA
Retrocopy LSCSEDMPIRYWDLGSFTNTVLYQGHACPVWDLGISPYSLYFASGSHDCTARLWSFDRTYPLRIYAGHLA

Parental  DVDCVKFHPNSNYLATGSTDKTVRLWSAQQGNSVRLFTGHRGPVLSLAFSPNGKYLASAGEDQRLKLWDL
          DV.CVKFHPNSNYLATGST.KTV.LWSAQ.GN.VRLFTGH.GPVLSLAFSPN.KYLASAG.DQRLKLWDL
Retrocopy DVACVKFHPNSNYLATGSTNKTVWLWSAQ*GNLVRLFTGHHGPVLSLAFSPNSKYLASAGKDQRLKLWDL

Parental  ASGTLYKELRGHTDNITSLTFSPDSGLIASASMDNSVRVWDIRNTYCSAPADGSSSELVGVYTGQMSNVL
          ASGTLYKELRGHTDNITSLTFSPDSGLIASASMDNSVRVWDIRN.YCS.PA.GSSSELVG.Y.GQMS..L
Retrocopy ASGTLYKELRGHTDNITSLTFSPDSGLIASASMDNSVRVWDIRNSYCSVPAYGSSSELVGLYIGQMSSIL

Parental  SVQFMACNLLLVTGITQENQEH
          S.QFMACN.LLVT.ITQENQEH
Retrocopy SMQFMACN-LLVT*ITQENQEH

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	0.00 RPM	6.12 RPM
SRP051959_heart	0.02 RPM	7.35 RPM
SRP051959_kidney	0.02 RPM	8.08 RPM
SRP051959_liver	0.00 RPM	6.22 RPM
SRP051959_lung	0.00 RPM	9.21 RPM
SRP051959_lymph_node	0.00 RPM	11.87 RPM
SRP051959_skeletal_muscle	0.00 RPM	4.80 RPM
SRP051959_spleen	0.06 RPM	11.76 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4042 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4042 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4042 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034225	1 retrocopy	retro_btau_1300,
Callithrix jacchus	ENSCJAG00000010986	1 retrocopy	retro_cjac_4042 ,
Homo sapiens	ENSG00000135801	1 retrocopy	retro_hsap_1750,
Gorilla gorilla	ENSGGOG00000028544	1 retrocopy	retro_ggor_2253,
Pan troglodytes	ENSPTRG00000002091	1 retrocopy	retro_ptro_1216,
Rattus norvegicus	ENSRNOG00000018027	1 retrocopy	retro_rnor_509,