RetrogeneDB ID: retro_cjac_3235

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:83306761..83308201(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CFLAR
• Ensembl ID: ENSCJAG00000004505
• Aliases: None
• Description: CASP8 and FADD-like apoptosis regulator [Source:HGNC Symbol;Acc:1876]

Sequence

>retro_cjac_3235
ATGTCTGCAGAGGTCATCCATCAGGTTGAAGAAGCACTTGACACAGATGAGAAGGAGATGCTGCTCTTTTTGTGCCGGGA
TGTTGCTATAGATGTGGTTCCACCTAATGTCAGGGACCTTCTGGATATTTTACGTGAAAGAGGTAAGCTCTCTCTCGTGA
GCTTGGCTGAACTGCTCTACAGAGTGAGGCGATTCGACCTGCTCAAGCGGATCTTGAAAATGGACAGAAAAGCCGTGGAG
GACCACCTGCTCAGGCACCCTCACCTTGTTTCGGACTACAGAGTGCTGATGGCAGAGATTGGTGAGAATTTGGATAAATC
TGATGTGTCCTCATGAATTTTCCTCATGAGGGATTATATGGACCGAGGCAAGAAAAACAAGGAGAAGAGTTTCTTGGACC
TTGTGGTTGAGTTGGAGAAACGAAATCTGGTTGCCCCAGATCAACTGGATTTATTAGAAAAAGGCCTAAAGAACATCCAC
AGATTAGACCTGAAGACAAAAATCCAGAAGTACAAGCAGTCTGCTCAAAGAGCAGGGACAAGTTACAAGAATGTTCTCCA
AGCAGCAATCAAAAACAGTTTCAAGGATCCTTCAAATAACTTCAGGCTCCATAATGGGAGAAGTAAAGAACAAAGACTTA
AGGAACAACTTGGCACTCAACAAGAACCAGTGAAGACATCCATTCAGGAATCAGAAGCTTTTTTGCCTCAGAGCATGCCT
GAAGAGAGATACAAGATGAAGAGCAAGCCCCTAGGAATCTGCCTGATAATCGATTGCATTGGCAATGAGACAGAGCTTCT
TCGAGATACCTTCACTTCCCTGGGCTATGAAGTTCAGAAATCCTTGCATCTCACTATGGATGGTATATTACAGGTTCTTC
AACGAGTTGCCTGTATGCCCCAACACCAAGACTACGACAGCTTTGTGTGTGTCCTGGTGAGCCGACGAGGCTCCCAGACT
GTGTATGGTGTGGATCAGACTCACCCAGGGCTCCCCCTGCATCACATCAGGAGGATGTTTATGAAAGATTTATGCCCTTA
TCTAGTAGGGAAGCCAAAGGTGTTTTTTATTCAGAACTATATGGTGTCAGAGGGCCAGCTGGAGGACAGCAGCCTCCTGG
AGGTGGATGGGCCAGCGATGAAGAATGTGGAATCCAAGTCTCAGCAGCGAGGGCTGTGCACAGTTCACCGAGAAGCTGAC
TTCTTCTGGAGCCTTTGCACTGCAGATGTGTCCCTGCTGGAAGAGTCCTGCAGTTCACCGTCCCTGTACCTGCAGTGCCT
CTCCCAGAAACTGAGACAAGAAAGAAAACGTCCACTCCTGGATCTCCACATTGAACTCAATAGCACCATGTATGATTGGA
ACAGCAGAGTTTCTGCTAAGGAGAAATACGATGTCTGGCTGCAGCACACTCTGAGAAAGAAACTTATCCTCTCTTACACA

Alignment

ORF - retro_cjac_3235 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.92 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSAEVIHQVEEALDTDEKEMLLFLCRDVAIDVVPPNVRDLLDILRERGKLSLVSLAELLYRVRRFDLLKR
          MSAEVIHQVEEALDTDEKEMLLFLCRDVAIDVVPPNVRDLLDILRERGKLSLVSLAELLYRVRRFDLLKR
Retrocopy MSAEVIHQVEEALDTDEKEMLLFLCRDVAIDVVPPNVRDLLDILRERGKLSLVSLAELLYRVRRFDLLKR

Parental  ILKMDRKAVEDHLLRHPHLVSDYRVLMAEIGENLDKSDVSSLIFLMRDYMGRGKINKEKSFLDLVVELEK
          ILKMDRKAVEDHLLRHPHLVSDYRVLMAEIGENLDKSDVSS.IFLMRDYM.RGK.NKEKSFLDLVVELEK
Retrocopy ILKMDRKAVEDHLLRHPHLVSDYRVLMAEIGENLDKSDVSS*IFLMRDYMDRGKKNKEKSFLDLVVELEK

Parental  RNLVAPDQLDLLEKCLKNIHRLDLKTKIQKYKQSAQGAGTSYKNVLQAAIKNSFKDPSNNFRLHNGRSKE
          RNLVAPDQLDLLEK.LKNIHRLDLKTKIQKYKQSAQ.AGTSYKNVLQAAIKNSFKDPSNNFRLHNGRSKE
Retrocopy RNLVAPDQLDLLEKGLKNIHRLDLKTKIQKYKQSAQRAGTSYKNVLQAAIKNSFKDPSNNFRLHNGRSKE

Parental  QRLKEQLGTQQEPVKTSIQESEAFLPQSMPEERYKMKSKPLGICLIIDCIGNETELLRDTFTSLGYEVQK
          QRLKEQLGTQQEPVKTSIQESEAFLPQSMPEERYKMKSKPLGICLIIDCIGNETELLRDTFTSLGYEVQK
Retrocopy QRLKEQLGTQQEPVKTSIQESEAFLPQSMPEERYKMKSKPLGICLIIDCIGNETELLRDTFTSLGYEVQK

Parental  SLHLTMDGILQVLQRVACMPQHQDYDSFVCVLVSRGGSQTVYGVDQTHPGLPLHHIRRMFMGDLCPYLVG
          SLHLTMDGILQVLQRVACMPQHQDYDSFVCVLVSR.GSQTVYGVDQTHPGLPLHHIRRMFM.DLCPYLVG
Retrocopy SLHLTMDGILQVLQRVACMPQHQDYDSFVCVLVSRRGSQTVYGVDQTHPGLPLHHIRRMFMKDLCPYLVG

Parental  KPKVFFIQNYMVSEGQLEDSSLLEVDGPAMKNVESKSQQRGPCTVHREADFFWSLCTADVSLLEESCGSP
          KPKVFFIQNYMVSEGQLEDSSLLEVDGPAMKNVESKSQQRG.CTVHREADFFWSLCTADVSLLEESC.SP
Retrocopy KPKVFFIQNYMVSEGQLEDSSLLEVDGPAMKNVESKSQQRGLCTVHREADFFWSLCTADVSLLEESCSSP

Parental  SLYLQCLSQKLRQERKRPLLDLHIELNSHMYDWNSRVSAKEKYDVWLQHTLRKKLILSYT
          SLYLQCLSQKLRQERKRPLLDLHIELNS.MYDWNSRVSAKEKYDVWLQHTLRKKLILSYT
Retrocopy SLYLQCLSQKLRQERKRPLLDLHIELNSTMYDWNSRVSAKEKYDVWLQHTLRKKLILSYT

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	0.07 RPM	42.13 RPM
SRP051959_heart	0.04 RPM	30.54 RPM
SRP051959_kidney	0.11 RPM	43.40 RPM
SRP051959_liver	0.17 RPM	68.71 RPM
SRP051959_lung	0.18 RPM	69.84 RPM
SRP051959_lymph_node	0.39 RPM	92.01 RPM
SRP051959_skeletal_muscle	0.04 RPM	23.39 RPM
SRP051959_spleen	0.08 RPM	78.28 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3235 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3235 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3235 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004505	1 retrocopy	retro_cjac_3235 ,
Monodelphis domestica	ENSMODG00000015097	1 retrocopy	retro_mdom_1986,
Mus musculus	ENSMUSG00000026031	1 retrocopy	retro_mmus_244,