RetrogeneDB ID: retro_cjac_1974

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:160432541..160434068(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023404
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TRMT5
• Ensembl ID: ENSCJAG00000019157
• Aliases: None
• Description: tRNA methyltransferase 5 [Source:HGNC Symbol;Acc:23141]

Sequence

>retro_cjac_1974
ATGGTGCTTTGGATCTTATGGAGGCCATTTGGATTCTCAAGAAGACTTCTGAAACCGGGAAGCCATAGCATAACTGAATC
AAAATCATTAATTCCACTAGCTTGGACATCCCTGACACAGACGCTTTCAGAAGCACCTGGTATTCTCTTATTGGGTCAAA
GAAAAATATTCTCAACCATGCCAGAAATAGAAACACATGAGAGAGACTCTGAATTGTTTTCACCACCCTCTGATGTCCGA
GGCATGACAAAACTTGATAGAACAGCTTTTAAAAAGACAGTCAGCATTCCAGTGCTTAAAGTGAGGAAAGAAGTAGTCAG
TAAATTGATGCGATCCCTTAAAAGGGCAGCATTGCAGCGCCCAGGTGTAAAACGTGTAATTGAAGATCCAGAAGATAAAG
AAAGTAGACTAATCATGTTGGATCCCTATAAAATGTTTACTCATGATTCCTTTGAGGAAGCAGAACTCAGTGTTTTAGAG
CAGTTAAATGTCAGTCCACAGATCTCTGAATATAATTTGGAACTAACATACGAAAACTTTAAGTCAGAAGAGATCTTGAG
AGCTGTGCTTCCTGAAGGTCAAGATGTAACTTCAGGGTTTAGCAGAGTTGGACATATTGCACACCTGAACCTTCGAGATC
ATCAGCTACCTTTCAAACATTTAATTGGCCAGGTTATGATTGACAAAAATCCAGGAATCACCTCAGCAGTAAATAAAATA
AATAATATTGACAATATGTACCGAAATTTCCAAATGGAAGTGCTATCTGGAGAACAGAACATGATGACAAAGGTTCGAGA
AAACAACTACACCTATGAGTTTGATTTTTCAAAAGTCTATTGGAATCCTCGTCTCTCTACAGAACACAGCCGTATCACAG
AACTTCTCAAGCCTGGGGATGTCCTATTTGATGTTTTTGCTGGGGTTGGGCCCTTTGCCATTCCAGTAGCAAAGAAAAAC
TGCACTGTATTTGCCAATGATCTCAATCCTGAATCCCATAAGTGGCTATTGCACAATTGTAAATTAAATAAAGTGGACCA
AAATGTGAAAGTCTTCAACTTGGATGGGAAGGACTTCCTCCAAGGACCCATCAAAGAAGAGTTAATGCAGCTGCTGAGTC
TGTCAAAAGAAAGAAAACCCTCTGTGCACATTGTCATGAATTTGCCAGCAAAAGCTATAGAGTTTCTTAGTGCTTTCAAA
ACACTTTTAGATGAGCAGCCATGCAGCAGTGAACTACTTCCCATAGTGCACTGTTACAGCTTTTCCAAAGATGCTAACCC
TACTGAAGACGTTCGTCAAAGAGCTGGAGCTGTGTTAGGCATTTCACTGGAGGCATGCAGTTCAGTTCACCTGGTAAGAA
ATGTGGCCCCAAACAAGGAAATGCTGTGCATCACCTTTCAGATTCCTGCTGCTGTACTCTACAAGAACCAGACCAGAAAT
CCAGAGAATTGCGAAGATCCGCCTCTTAAAAGGCAGAGGACAGCTGAAGCCTTTTCAGATGAAAAAACACAAATTGCTTC
AAACACT

Alignment

ORF - retro_cjac_1974 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.02 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVLRILWRPFGFSRRLVKLGSHSITESKSLIPLAWTSLTQTLSEAPGILLLGQRKIFSTMPEIETHERDS
          MVL.ILWRPFGFSRRL.K.GSHSITESKSLIPLAWTSLTQTLSEAPGILLLGQRKIFSTMPEIETHERDS
Retrocopy MVLWILWRPFGFSRRLLKPGSHSITESKSLIPLAWTSLTQTLSEAPGILLLGQRKIFSTMPEIETHERDS

Parental  ELFSPPSDVRGMTKLDRTAFKKTVSIPVLKVRKEVVSKLMRSLKRAALQRPGVKRVIEDPEDKESRLIML
          ELFSPPSDVRGMTKLDRTAFKKTVSIPVLKVRKEVVSKLMRSLKRAALQRPGVKRVIEDPEDKESRLIML
Retrocopy ELFSPPSDVRGMTKLDRTAFKKTVSIPVLKVRKEVVSKLMRSLKRAALQRPGVKRVIEDPEDKESRLIML

Parental  DPYKMFTHDSFEEAELSVLEQLNVSPQISEYNLELTYENFKSEEILRAVLPEGQDVTSGFSRVGHIAHLN
          DPYKMFTHDSFEEAELSVLEQLNVSPQISEYNLELTYENFKSEEILRAVLPEGQDVTSGFSRVGHIAHLN
Retrocopy DPYKMFTHDSFEEAELSVLEQLNVSPQISEYNLELTYENFKSEEILRAVLPEGQDVTSGFSRVGHIAHLN

Parental  LRDHQLPFKHLIGQVMIDKNPGITSAVNKINNIDNTYRNFQMEVLSGEQNMMTKVRENNYTYEFDFSKVY
          LRDHQLPFKHLIGQVMIDKNPGITSAVNKINNIDN.YRNFQMEVLSGEQNMMTKVRENNYTYEFDFSKVY
Retrocopy LRDHQLPFKHLIGQVMIDKNPGITSAVNKINNIDNMYRNFQMEVLSGEQNMMTKVRENNYTYEFDFSKVY

Parental  WNPRLSTEHSRITELLKPGDVLFDVFAGVGPFAIPVAKKNCTVFANDLNPESHKWLLHNCKLNKVDQNVK
          WNPRLSTEHSRITELLKPGDVLFDVFAGVGPFAIPVAKKNCTVFANDLNPESHKWLLHNCKLNKVDQNVK
Retrocopy WNPRLSTEHSRITELLKPGDVLFDVFAGVGPFAIPVAKKNCTVFANDLNPESHKWLLHNCKLNKVDQNVK

Parental  VFNLDGKDFLQGPIKEELMQLLSLSKERKPSVHIVMNLPAKAIEFLSAFKSLLDEQPCSSELLPIVHCYS
          VFNLDGKDFLQGPIKEELMQLLSLSKERKPSVHIVMNLPAKAIEFLSAFK.LLDEQPCSSELLPIVHCYS
Retrocopy VFNLDGKDFLQGPIKEELMQLLSLSKERKPSVHIVMNLPAKAIEFLSAFKTLLDEQPCSSELLPIVHCYS

Parental  FSKDANPTEDVRQRAGAVLGISLEACSSVHLVRNVAPNKEMLCITFQIPAAVLYKNQTRNPENCEDPPLK
          FSKDANPTEDVRQRAGAVLGISLEACSSVHLVRNVAPNKEMLCITFQIPAAVLYKNQTRNPENCEDPPLK
Retrocopy FSKDANPTEDVRQRAGAVLGISLEACSSVHLVRNVAPNKEMLCITFQIPAAVLYKNQTRNPENCEDPPLK

Parental  RQRTAEAFSDEKTQIASNT
          RQRTAEAFSDEKTQIASNT
Retrocopy RQRTAEAFSDEKTQIASNT

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	0.04 RPM	4.30 RPM
SRP051959_heart	0.12 RPM	3.74 RPM
SRP051959_kidney	0.20 RPM	5.01 RPM
SRP051959_liver	0.02 RPM	5.57 RPM
SRP051959_lung	0.15 RPM	4.42 RPM
SRP051959_lymph_node	0.16 RPM	3.63 RPM
SRP051959_skeletal_muscle	0.09 RPM	5.31 RPM
SRP051959_spleen	0.40 RPM	5.48 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1974 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1974 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1974 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011796	1 retrocopy	retro_btau_405,
Callithrix jacchus	ENSCJAG00000019157	1 retrocopy	retro_cjac_1974 ,