RetrogeneDB ID: retro_cjac_2276

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:133026891..133028108(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000002418
• Aliases: None
• Description: None

Sequence

>retro_cjac_2276
ATGCCTTGCACTTGTACCTGGAGGAACTGGAGACAGTGGATGCGACCATTAGCAGTGGTCATCTACCTGGTGTCCATAGT
GGTTGCAGTTCCCCTATGCCTCTGGGAATCACAGAAACTGGAGGTTGGAATACACACCAGGGCTTGGTTTACTGCTGGGA
TCTTTATGCTATTGACTATACCTATATCACTCTGGGTGATATTGCAACACTTAGTGCATTGTATACAACCTGAACTATAA
AAATCAATAAAAAGTATTCTTTGGATGGTACTCATTTACAGTTTAGATAGTTGGATAGCGTTGAAATATCCCAGCATTGC
AATATGAGTATAACTGCAGGGAATGCTATGAAGCTTATGTAATTTACAACTTTGTGAATTCCTTACCAATGACCTAACTA
ACCGGTACCCAAATCTGGTATTAATCCTTGAAGCCAAAGATCAGCAGAAACACTGCCCTCCTTTATGTTGCTGTCCACCA
TTGGCTATGGGAGAAGTATTGCTGTTTAGGAGCAAACTAGGTGTATTGTGGTACACAGTCGTCAGACCTTTCACCACCAT
TATTGCTTTAATCTGCAGGTTGCTTGGTATATATGATGAAGGGAACTTTAGCTTTTCAAATGTTTGGACTTACTTGGTTA
TAATGAACATGTCACAGTTCTTTGTCATGTATTGTCTCCTGCTATTTTATAAAGTACTAAGGGAAGAACTGAGCCCAATC
CAACGTGTTGGCAAATTTCTTTGTGTAAAGCTGGTGGTTTTTGTTTCTTTTTGGCAAGAGTAGTTATTGCTTTGTTGGTA
AAAATTGGTGTTATTTCTGAAAAGCATAAGTGGGAATGGCAAACTGTAGAAGCTGTGGTCACAGGACTCCAGGACTTTAT
TATTGAGATATTCCTCACTGCCATTGCTCATCATTACACATTCTCATATAAACCATATGTCCGAGAAGCAGAAGAAGGCT
CATGCTTTGATCCCTTTCTTGCCATGTGGGATGTCTCAGATATTAGAGACGAGATTTCTGAACAAGTAAGGCATGTTGGA
CGGACAGTCAGGGGACATCCCAGGAAAAAATTGTTTCCCGAGGATCAAGATCAAAATGAACATACAAGCTTATTATCATC
ATCATCACAAGATGTAATTTCCATTGTTTCTTGTATGCCACCTTCACCCATGGGTTACTACCAAGGGTTTGGACACACTG
TAACTCCAGACTTCACC

Alignment

ORF - retro_cjac_2276 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.2 %
• Parental protein coverage: 93.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPCTCTWRNWRQWIRPLAVVLYLVSIVVAVPLCVWELQKLEVGIHTKAWFIAGIFLLLTIPISLWVILQH
          MPCTCTWRNWRQW.RPLAVV.YLVSIVVAVPLC.WE.QKLEVGIHT.AWF.AGIF.LLTIPISLWVILQH
Retrocopy MPCTCTWRNWRQWMRPLAVVIYLVSIVVAVPLCLWESQKLEVGIHTRAWFTAGIFMLLTIPISLWVILQH

Parental  LVHYTQPELQKPIMRILWMVPIYSLDSWIALKY-PSIAIYVDTCRECYEAYVIYNFMG-FLTNYLTNRYP
          LVH..QPEL.K.I..ILWMV.IYSLDSWIALKY.P....Y...CRECYEAYVIYNF...FLTN.LTNRYP
Retrocopy LVHCIQPEL*KSIKSILWMVLIYSLDSWIALKY>PALQ-YEYNCRECYEAYVIYNFVN<FLTNDLTNRYP

Parental  NLVLILEAKDQQKHFPPLCCCPPWAMGEVLLFRCKLGVLQYTVVRPFTTIVALICELLGIYDEGNFSFSN
          NLVLILEAKDQQKH.PPLCCCPP.AMGEVLLFR.KLGVL.YTVVRPFTTI.ALIC.LLGIYDEGNFSFSN
Retrocopy NLVLILEAKDQQKHCPPLCCCPPLAMGEVLLFRSKLGVLWYTVVRPFTTIIALICRLLGIYDEGNFSFSN

Parental  AWTYLVIINNMSQLFAMYCLLLFYKVLKEELSPIQPVGKFLCVKLVVFVSFWQA-VVIALLVKVGVISEK
          .WTYLVI.N.MSQ.F.MYCLLLFYKVL.EELSPIQ.VGKFLCVKLVVFVSFWQ..VVIALLVK.GVISEK
Retrocopy VWTYLVIMN-MSQFFVMYCLLLFYKVLREELSPIQRVGKFLCVKLVVFVSFWQE<VVIALLVKIGVISEK

Parental  HTWEWQTVEAVATGLQDFIICIEMFLAAIAHHYTFSYKPYVQEAEEGSCFDSFLAMWDVSDIRDDISEQV
          H.WEWQTVEAV.TGLQDFII..E.FL.AIAHHYTFSYKPYV.EAEEGSCFD.FLAMWDVSDIRD.ISEQV
Retrocopy HKWEWQTVEAVVTGLQDFII--EIFLTAIAHHYTFSYKPYVREAEEGSCFDPFLAMWDVSDIRDEISEQV

Parental  RHVGRTVRGHPRKKLFPEDQDQNEHTSLLSSSSQDAISIASSMPPSPMGHYQGFGHTVTPQTT
          RHVGRTVRGHPRKKLFPEDQDQNEHTSLLSSSSQD.ISI.S.MPPSPMG.YQGFGHTVTP..T
Retrocopy RHVGRTVRGHPRKKLFPEDQDQNEHTSLLSSSSQDVISIVSCMPPSPMGYYQGFGHTVTPDFT

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	18.55 RPM
SRP051959_heart	0.11 RPM	13.61 RPM
SRP051959_kidney	0.02 RPM	24.87 RPM
SRP051959_liver	0.00 RPM	18.95 RPM
SRP051959_lung	0.03 RPM	19.20 RPM
SRP051959_lymph_node	0.00 RPM	13.38 RPM
SRP051959_skeletal_muscle	0.00 RPM	13.80 RPM
SRP051959_spleen	0.02 RPM	15.86 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2276 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2276 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2276 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002418	1 retrocopy	retro_cjac_2276 ,
Felis catus	ENSFCAG00000015410	2 retrocopies	retro_fcat_1929, retro_fcat_755,
Homo sapiens	ENSG00000164168	1 retrocopy	retro_hsap_4870,
Macaca mulatta	ENSMMUG00000004977	1 retrocopy	retro_mmul_2611,
Otolemur garnettii	ENSOGAG00000015819	1 retrocopy	retro_ogar_3118,
Tarsius syrichta	ENSTSYG00000005633	1 retrocopy	retro_tsyr_1001,