RetrogeneDB ID: retro_cjac_1547

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 17:30089110..30089924(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000034889
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPHLN1
• Ensembl ID: ENSCJAG00000017726
• Aliases: None
• Description: None

Sequence

>retro_cjac_1547
CATCCCAGTGATGAATCTGGTTATAGATGGACAAGAGATGATCATTCTGCAAGCAGGCAACCTGAATACAGGGACATGAG
AGATGGCTTTAGAAGAAAAAGTTTCTACTCTTCCCATTTTGCAAGAGAACGGTCTCCTCATAAAAGAGACAATGCTTTTT
TCCAAGAATCACATGGTGGCCAAAAGGATTCTCCACACAGCAGATCTGACTCCATTGTCAGTAGCAGAAGCTTCTCTCCA
GAAAGGAGCAAATCATACCTTTCCATCAGTCTCAACATGGGAACAAAGAGAGCCCTGCCCAGTCTTTGAAAACATCAAGA
GATACTTCACCCTCAAGTGCTTCAGTGGCTTCTTCATCAAAGGTGTTAGGCAAACCCAGTAGGCTAACTGAAAAGGAACT
TGCTGAGGCTGCAAGCAAGTGGGCTGCTGAAAAGCTAGAGAAAGCAGATGAAAGTAATTTGCCTGAAATTTCTGAGTATG
AGGCAGGATCCACAGCACCATTATTTACTGACCAGACAGAGGAACCTAAGTCAAACACAGCAGATGCCATAGAATTATTT
GAAAATAGTCAGCTAACCAGTCGCTCTAAAGCAATAGCATCAAAAACAAAGAGATTGAACAGGTTTACCAACAAGACTGT
GAAACTTTCGGGATGGTGGTGAAAATGCTGATTGAAAAAGATCCTTCATTAGAAAAGTCTATACAGTTTGCATTGAGGCA
GAATTTACATGAAATAGGTGAGCGGTGTGTTGAAGAACTCAAGGATTTCATTGCAGAATATGATATTTCCGCTCAAGATT
TTGGAGAGCCTTTC

Alignment

ORF - retro_cjac_1547 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.61 %
• Parental protein coverage: 78.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HRGDESGYRWTRDDHSASRQPEYRDMRDGFRRKSFYSSHYARERSPHKRDNAFFRESPGGRKDSPHSRSG
          H..DESGYRWTRDDHSASRQPEYRDMRDGFRRKSFYSSH.ARERSPHKRDNAFF.ES.GG.KDSPHSRS.
Retrocopy HPSDESGYRWTRDDHSASRQPEYRDMRDGFRRKSFYSSHFARERSPHKRDNAFFQESHGGQKDSPHSRSD

Parental  SSVSSRSYSPERSKSY-SFHQSQHRNKERPAQSLKTSRDTSPSSASAASSSKVLDKPSRLTEKELAEAAS
          S.VSSRS.SPERSKSY..FHQSQH.NKE.PAQSLKTSRDTSPSSAS.ASSSKVL.KPSRLTEKELAEAAS
Retrocopy SIVSSRSFSPERSKSY<PFHQSQHGNKESPAQSLKTSRDTSPSSASVASSSKVLGKPSRLTEKELAEAAS

Parental  KWAAEKLEKADESNLPEISEYEAGSTAPLFTDQPEEPESNTADAIELFEDSQLTSRSKAIASKT-KEIEQ
          KWAAEKLEKADESNLPEISEYEAGSTAPLFTDQ.EEP.SNTADAIELFE.SQLTSRSKAIASKT.KEIEQ
Retrocopy KWAAEKLEKADESNLPEISEYEAGSTAPLFTDQTEEPKSNTADAIELFENSQLTSRSKAIASKT<KEIEQ

Parental  VYRQDCETFGMVVKMLIEKDPSLEKSIQFALRQNLHEIGERCVEELKHFIAEYDTSTQDFGEPF
          VY.QDCETFGMVVKMLIEKDPSLEKSIQFALRQNLHEIGERCVEELK.FIAEYD.S.QDFGEPF
Retrocopy VYQQDCETFGMVVKMLIEKDPSLEKSIQFALRQNLHEIGERCVEELKDFIAEYDISAQDFGEPF

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	22.68 RPM
SRP051959_heart	0.02 RPM	27.52 RPM
SRP051959_kidney	0.02 RPM	28.73 RPM
SRP051959_liver	0.00 RPM	21.47 RPM
SRP051959_lung	0.02 RPM	28.52 RPM
SRP051959_lymph_node	0.05 RPM	30.91 RPM
SRP051959_skeletal_muscle	0.00 RPM	20.09 RPM
SRP051959_spleen	0.04 RPM	31.79 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1547 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1547 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1547 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010693	1 retrocopy	retro_chof_1231,
Callithrix jacchus	ENSCJAG00000017726	1 retrocopy	retro_cjac_1547 ,
Cavia porcellus	ENSCPOG00000012266	2 retrocopies	retro_cpor_744, retro_cpor_745,
Dasypus novemcinctus	ENSDNOG00000002007	1 retrocopy	retro_dnov_1790,
Equus caballus	ENSECAG00000016067	1 retrocopy	retro_ecab_209,
Mus musculus	ENSMUSG00000036167	3 retrocopies	retro_mmus_1657, retro_mmus_3561, retro_mmus_79,
Otolemur garnettii	ENSOGAG00000004012	2 retrocopies	retro_ogar_1387, retro_ogar_2103,
Tarsius syrichta	ENSTSYG00000010740	1 retrocopy	retro_tsyr_2044,