RetrogeneDB ID: retro_cjac_2561

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:115225878..115226935(+)
• Located in intron of: ENSCJAG00000000333

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARG2
• Ensembl ID: ENSCJAG00000015277
• Aliases: None
• Description: None

Sequence

>retro_cjac_2561
ATGTCCTTAAGGGGCAGTCTCTCGCGTCTCCTCCAGACGCGAGTGCATTCCATCCTGAAGAAATCCATCCACTCCGTGGC
TGTCATAGGAGCCCCGTTCTCACAAGGGCAGAAAAGAAAAGGAGTGGAGCATGGTCCCACTGCCATAAGAGAAGCTGGCC
TGATGAAAAGGCTCTCCAGTTTGGGCTGCCACCTAAAAGACTTTGGAGATTTGAGTTTTACTGCAGTTCCCAAAGATGAT
CTCTACAACAACGTAATAGTGAATCCATGCTCAGTGGGTCTTGCCAACCAGGAACTGGCTGAGGTGGTTAGTAGAGCTGT
GTCAGATGGCTACAGCTGTGTCACATTGGGAGGAGACCACAGCCTGGCAATCGGTACCATTAGTGGTCATGCCCGACACT
GCCCAGACTTTTGCATTATCTGGGTTGATGCCCAAGCTGACATCAACACACCCCTTACCACTTCATCAGGAAATCTCCAT
GGACAGCCAGTTTCATTTCTCCTCAGAGAACTACAGGACAAGATACCACAACTCCCAGGATTTTCTTGGATCAAACCTTG
TATCTCTTCCCCAAGTATTGTGTATATTGGTCTAAGAGACGTGGATCCTCCTGAACATTTTATTTTAAAGAACTATGATA
TCCAGTAATTTTCCATGAGAGATATTGATCAACTCAGTATCCAGAAGGTCATGGAAAAAACATTTGATCTGCTGATTGGC
AAGAGACAAAGACCAATCCATCTGAGTTTTGATATTGATGCATTTGACCCTACATTGGCTCCAGCCCCAGGAACTCTTGT
GGTAGGAGGACTAACCTATCGAGAAGGCATGTATATTGCTGAGGAAATACACAATACAGGGTTGTTGTCGGCACTGGATC
TTGTTGAAGTCAATCCTCAGTTAGCCACCTCAGAGAAAGAGGCAAAGACTACAGCTAACCTGGCAGTGGATGTGATTGCT
TCAAGTTTTGGTCAGACAAGGGAAGGAGGGCACATTGTCTATGACCAATACTCCCAGTTCACCAGATGAATCGGAAAATC
AAGCACGTGTGAGAATT

Alignment

ORF - retro_cjac_2561 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.39 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSLRGSLSRLLQTRVHSILKKSVHSVAVIGAPFSQGQKRKGVEHGPAAIREAGLMKRLSSLGCHLKDFGD
          MSLRGSLSRLLQTRVHSILKKS.HSVAVIGAPFSQGQKRKGVEHGP.AIREAGLMKRLSSLGCHLKDFGD
Retrocopy MSLRGSLSRLLQTRVHSILKKSIHSVAVIGAPFSQGQKRKGVEHGPTAIREAGLMKRLSSLGCHLKDFGD

Parental  LSFTPVPKDDLYNNLIVNPRSVGLANQELAEVVSRAVSDGYSCVTLGGDHSLAIGTISGHARHCPDLCVI
          LSFT.VPKDDLYNN.IVNP.SVGLANQELAEVVSRAVSDGYSCVTLGGDHSLAIGTISGHARHCPD.C.I
Retrocopy LSFTAVPKDDLYNNVIVNPCSVGLANQELAEVVSRAVSDGYSCVTLGGDHSLAIGTISGHARHCPDFCII

Parental  WVDAHADINTPLTTSSGNLHGQPVSFLLRELQDKVPQLPGFSWIKPCISSPSIVYIGLRDVDPPEHFILK
          WVDA.ADINTPLTTSSGNLHGQPVSFLLRELQDK.PQLPGFSWIKPCISSPSIVYIGLRDVDPPEHFILK
Retrocopy WVDAQADINTPLTTSSGNLHGQPVSFLLRELQDKIPQLPGFSWIKPCISSPSIVYIGLRDVDPPEHFILK

Parental  NYDIQYFSMRDIDRLGIQKVMEQTFDLLIGKRQRPIHLSFDIDAFDPTLAPATGTPVVGGLTYREGMYIA
          NYDIQ.FSMRDID.L.IQKVME.TFDLLIGKRQRPIHLSFDIDAFDPTLAPA.GT.VVGGLTYREGMYIA
Retrocopy NYDIQ*FSMRDIDQLSIQKVMEKTFDLLIGKRQRPIHLSFDIDAFDPTLAPAPGTLVVGGLTYREGMYIA

Parental  EEIHNTGLLSALDLVEVNPQLATSEEEAKTTANLAVDVIASSFGQTREGGHIVYDQ-LPTPSSPDESENQ
          EEIHNTGLLSALDLVEVNPQLATSE.EAKTTANLAVDVIASSFGQTREGGHIVYDQ..P......E...Q
Retrocopy EEIHNTGLLSALDLVEVNPQLATSEKEAKTTANLAVDVIASSFGQTREGGHIVYDQ>TPSSPDESEN--Q

Parental  ARVRI
          ARVRI
Retrocopy ARVRI

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	5.48 RPM	4.64 RPM
SRP051959_heart	1.33 RPM	4.91 RPM
SRP051959_kidney	1.93 RPM	50.56 RPM
SRP051959_liver	1.99 RPM	17.61 RPM
SRP051959_lung	2.20 RPM	4.83 RPM
SRP051959_lymph_node	1.99 RPM	4.75 RPM
SRP051959_skeletal_muscle	1.09 RPM	9.46 RPM
SRP051959_spleen	3.82 RPM	5.23 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2561 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2561 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2561 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005722	1 retrocopy	retro_acar_91,
Choloepus hoffmanni	ENSCHOG00000007159	1 retrocopy	retro_chof_1179,
Callithrix jacchus	ENSCJAG00000015277	4 retrocopies	retro_cjac_1933, retro_cjac_2357, retro_cjac_2561 , retro_cjac_902,
Dasypus novemcinctus	ENSDNOG00000004808	1 retrocopy	retro_dnov_251,
Homo sapiens	ENSG00000081181	1 retrocopy	retro_hsap_3501,
Gorilla gorilla	ENSGGOG00000005615	1 retrocopy	retro_ggor_2367,
Monodelphis domestica	ENSMODG00000009978	1 retrocopy	retro_mdom_257,
Nomascus leucogenys	ENSNLEG00000000741	2 retrocopies	retro_nleu_2875, retro_nleu_792,
Oryctolagus cuniculus	ENSOCUG00000000584	1 retrocopy	retro_ocun_277,
Pongo abelii	ENSPPYG00000005926	1 retrocopy	retro_pabe_2893,
Pan troglodytes	ENSPTRG00000006467	1 retrocopy	retro_ptro_2373,