RetrogeneDB ID: retro_cjac_943

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:118930052..118931228(-)
• Located in intron of: ENSCJAG00000018509

Retrocopy information

• Ensembl ID: ENSCJAG00000018502
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GFPT2
• Ensembl ID: ENSCJAG00000010359
• Aliases: None
• Description: None

Sequence

>retro_cjac_943
TCCATTCACCGGGTCAAGCGCTCGGCTAGTGATGACCCATCTCGAGCCATCCAGACCTTGCAGATGGAACTGCAGCAAAT
CATGAAAGGTAACTTCAGTGCATTTATGCAGAAGGAGATCTTCGAACAGCCAGAATCCGTTTTCAATACTATGAGAGGTC
GGGTGAATTTTGAGACCAACACAGTGCTCCTGGGTGGCTTGAAGGACCACTTGAAGGAGATCCGACGATGCCGACGGCTC
ATCGTGATTGGCTGTGGAACCAGCTACCACGCTGCTGTGGCTACGCGGCAAGTTTTGGAGGAACTGACTGAGCTCCCTGT
GATGGTTGAACTTTCTAGCGATTTTCTGGACAGAAACACACCTGTGTTCAGGGATGATGTTTGCTTTTTCATCAGCCAGT
CAGGCGAGACGGCGGACACACTCTTGGCGCTGCGCTACTGCAAAGACCGCTGCGCCCTGACTGTGGGTGTTACCAACACC
GTGGGCAGCTCCATCTCCCGAGAGACCGACTGCGGCGTCCACATCAACGCAGGGCCAGAGATCGGTGTGGCCAGCACCAA
GGCTTATACCAGTCAGTTCATCTCTCTGGTGATGTTTGGTTTGATGATGTCTGAAGACCGAATTTCACTACAAAACAGGA
GGCAAGAGATCATCCGTGGTTTGAGATCTTTACCTGAGCTGATCAAGGAAGTGCTGTCACTGGATGAGAAGATTCATGAC
TTAGCCCTGGAGCTCTACACGCAGAGGTCACTCCTGGTGATGGGGCGGGGCTACAACTATGCCACCTGCCTGGAAGGAGC
CCTGAAAATTAAAGAGATAACCTACATGCACTCAGAAGGCATCCTGGCTGGGGAGCTGAAGCACGGGCCCCTGGCATTGA
TTGACAAGCAGATGCCCGTCATCATGGTCATCATGAAGGATCCTTGCTTTGCCAAATGCCAGAATGCCCTGCAGCAGGTC
ACGACCCGCCAGGGTCGCCCCATTATATTGTGCTCCAAGGATGATACTGAAAGTTCCAAGTTTGCGTATAAGACGATTGA
GCTGCCCCACACTGTGGACTGCCTCCAGGGCATCCTGAGCGTGATTCCGCTGCAGCTTCTATCCTTCCACCTGGCTGTCC
TCCGAGGATATGACGTTGACTTTCCCAGAAATCTGGCCAAGTCTGTAACTGTGGAA

Alignment

ORF - retro_cjac_943 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.23 %
• Parental protein coverage: 57.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SIHRVKRSASDDPSRAIQTLQMELQQIMKGNFSAFMQKEIFEQPESVFNTMRGRVNFETNTVLLGGLKDH
          SIHRVKRSASDDPSRAIQTLQMELQQIMKGNFSAFMQKEIFEQPESVFNTMRGRVNFETNTVLLGGLKDH
Retrocopy SIHRVKRSASDDPSRAIQTLQMELQQIMKGNFSAFMQKEIFEQPESVFNTMRGRVNFETNTVLLGGLKDH

Parental  LKEIRRCRRLIVIGCGTSYHAAVATRQVLEELTELPVMVELASDFLDRNTPVFRDDVCFFISQSGETADT
          LKEIRRCRRLIVIGCGTSYHAAVATRQVLEELTELPVMVEL.SDFLDRNTPVFRDDVCFFISQSGETADT
Retrocopy LKEIRRCRRLIVIGCGTSYHAAVATRQVLEELTELPVMVELSSDFLDRNTPVFRDDVCFFISQSGETADT

Parental  LLALRYCKDRRALTVGVTNTVGSSISRETDCGVHINAGPEIGVASTKAYTSQFISLVMFGLMMSEDRISL
          LLALRYCKDR.ALTVGVTNTVGSSISRETDCGVHINAGPEIGVASTKAYTSQFISLVMFGLMMSEDRISL
Retrocopy LLALRYCKDRCALTVGVTNTVGSSISRETDCGVHINAGPEIGVASTKAYTSQFISLVMFGLMMSEDRISL

Parental  QNRRQEIIRGLRSLPELIKEVLSLDEKIHDLALELYTQRSLLVMGRGYNYATCLEGALKIKEITYMHSEG
          QNRRQEIIRGLRSLPELIKEVLSLDEKIHDLALELYTQRSLLVMGRGYNYATCLEGALKIKEITYMHSEG
Retrocopy QNRRQEIIRGLRSLPELIKEVLSLDEKIHDLALELYTQRSLLVMGRGYNYATCLEGALKIKEITYMHSEG

Parental  ILAGELKHGPLALIDKQMPVIMVIMKDPCFAKCQNALQQVTARQGRPIILCSKDDTESSKFAYKTIELPH
          ILAGELKHGPLALIDKQMPVIMVIMKDPCFAKCQNALQQVT.RQGRPIILCSKDDTESSKFAYKTIELPH
Retrocopy ILAGELKHGPLALIDKQMPVIMVIMKDPCFAKCQNALQQVTTRQGRPIILCSKDDTESSKFAYKTIELPH

Parental  TVDCLQGILSVIPLQLLSFHLAVLRGYDVDFPRNLAKSVTVE
          TVDCLQGILSVIPLQLLSFHLAVLRGYDVDFPRNLAKSVTVE
Retrocopy TVDCLQGILSVIPLQLLSFHLAVLRGYDVDFPRNLAKSVTVE

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	3.82 RPM
SRP051959_heart	0.09 RPM	22.49 RPM
SRP051959_kidney	0.02 RPM	2.44 RPM
SRP051959_liver	0.00 RPM	1.17 RPM
SRP051959_lung	0.00 RPM	4.05 RPM
SRP051959_lymph_node	0.00 RPM	3.68 RPM
SRP051959_skeletal_muscle	0.00 RPM	6.66 RPM
SRP051959_spleen	0.00 RPM	2.50 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_943 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_943 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_943 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
Callithrix jacchus	ENSCJAG00000010359	1 retrocopy	retro_cjac_943 ,
Microcebus murinus	ENSMICG00000015921	1 retrocopy	retro_mmur_896,