RetrogeneDB ID: retro_cjac_2367

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:110408971..110410199(+)
• Located in intron of: ENSCJAG00000005299

Retrocopy information

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

Parental gene information

• Parental gene symbol: SKP2
• Ensembl ID: ENSCJAG00000018275
• Aliases: None
• Description: None

Sequence

>retro_cjac_2367
GTGCACAGGAAGCACCTCCAGGAGATTCCAGTCCTGAGTAGCAACGTTGCCACTAGCTTCACGTGGGGATGGGATTCCAG
CAAGACTTCTGAACTGCTCTCAGGCATGGGGGTCTCCGCCCCGGAGAAAGAGGAGCCCGACAGTGAGAATATCCCCCAGG
AACTGCTCTCAAACCTGGGCCTCCAGCAGAGCCCCCCAAGGAAACGGCTGAAGAGCAAAGGGAGTGACAAAGACTTTGTG
GTTATCCCCAGGCCTAAGCTAAATCGAGAGAACTTTCCAGGTGTTTCATGGGACTCCCTTCCGGATGAGCTGCTTTTGGG
GATCTTTTCCTGTCTGTGCCTCCCTGAGCTGCTAAAGGTCTCTGGTGTTTTTAAGAGGTGGTTTCGCCTAGCGTTTGACG
AGTCTCTATGGCAAACCTTAGACCTCACAGGTAAAAGTCTGCACCTGGATGTGACTGGTCCGTTGCTGTCTCAAGGGGTG
ACTGCCTTCCGCTGCCCACGATCATTTACAGACCAACCATTAGCTGAACATTTCAGCCCTTTTCGTGTGCAGCACATGGG
CCTGTCAAACTCAGTTACTGAAGTGTCCACCCTCCAGGGCATTCTGTCTCAGTGTTCCAAGTTGCAGAATCTAAGCCTGG
AAGGTCTGCGGCTGTCAGAGCCCATTGTCAATAATCTCGTACAAAACTCGAATTTAGTTCGACTTAACCTTTGTAGGTGT
TCTGGATTCTCTTAATTTGCCCTGCAGACTTTGCTAAGTGGCTGTTCCAGACTGGATGAGCTGAACCTTTCCTGGTACTT
TGATTTCACTGAGAAGCATGTGTAGTTGGCTGTTGCGCACGTGTCAGAGACCATCACCCCGCTGAATCTTAGCGGCTACA
GAAAGAATCTCCAGAAATCACATCTTTCTACTTTAGTTAGAAGATGCTCCAATCTTGTCCACCTAGACTTAAGTGATAGT
ATCATGCTAAAGTATGACTGCTTCCCGGAATTTTTCCAGCTCAACTAACTCCAACAACACCTGTCTCTCAGTCGGTGCTA
TGATATAATACCTGAAACTTTACTTGAACTCGGAGAAATTCCCACACTAAAAAACACTACAAGTTTTTGGAATTGTGCCA
GATGGTACCCTTCAACTGTTAAAGAAGGCCCTTCCTCATCTACAGATTAATTGCTCCCATTTCACCACCATTGCCAGGCC
AACTATTGACAACCAAAAGAACCAGGAG

Alignment

ORF - retro_cjac_2367 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.2 %
• Parental protein coverage: 96.23 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MHRKHLQEIPDLSSNVATSFTWGWDSSKTSELLSGMGVSALEKEEPDSENIPQELLSNLGIPQSPPRKRL
          .HRKHLQEIP.LSSNVATSFTWGWDSSKTSELLSGMGVSA.EKEEPDSENIPQELLSNLG..QSPPRKRL
Retrocopy VHRKHLQEIPVLSSNVATSFTWGWDSSKTSELLSGMGVSAPEKEEPDSENIPQELLSNLGLQQSPPRKRL

Parental  KSKGSDKDFVIIRRPKLNRENFPGVSWDSLPDELLLGIFSCLCLPELLKVSGVCRRWYRLAFDESLWQTL
          KSKGSDKDFV.I.RPKLNRENFPGVSWDSLPDELLLGIFSCLCLPELLKVSGV..RW.RLAFDESLWQTL
Retrocopy KSKGSDKDFVVIPRPKLNRENFPGVSWDSLPDELLLGIFSCLCLPELLKVSGVFKRWFRLAFDESLWQTL

Parental  DLTGKNLHPDVTGRLLSQGVIAFRCPRSFMDQPLAEHFSPFRVQHMDLSNSVIEVSTLQGILSQCSKLQN
          DLTGK.LH.DVTG.LLSQGV.AFRCPRSF.DQPLAEHFSPFRVQHM.LSNSV.EVSTLQGILSQCSKLQN
Retrocopy DLTGKSLHLDVTGPLLSQGVTAFRCPRSFTDQPLAEHFSPFRVQHMGLSNSVTEVSTLQGILSQCSKLQN

Parental  LSLEGLRLSDPIVNNLAQNSNLVRLNLCGCSGFSEFALQTLLSGCSRLDELNLSWCFDFTEKHVQVAVAH
          LSLEGLRLS.PIVNNL.QNSNLVRLNLC.CSGFS.FALQTLLSGCSRLDELNLSW.FDFTEKHV..AVAH
Retrocopy LSLEGLRLSEPIVNNLVQNSNLVRLNLCRCSGFS*FALQTLLSGCSRLDELNLSWYFDFTEKHV*LAVAH

Parental  VSETITQLNLSGYRKNLQKSDLSTLVRRCPNLVHLDLSDSIMLKNDCFPEFFQLNYL-QHLSLSRCYDII
          VSETIT.LNLSGYRKNLQKS.LSTLVRRC.NLVHLDLSDSIMLK.DCFPEFFQLN.L.QHLSLSRCYDII
Retrocopy VSETITPLNLSGYRKNLQKSHLSTLVRRCSNLVHLDLSDSIMLKYDCFPEFFQLN*LQQHLSLSRCYDII

Parental  PETLLELGEIPTL-KTLQVFGIVPDGTLQLLKEALPHLQINCSHFTTIARPTIDNQKNQE
          PETLLELGEIPTL.KTLQVFGIVPDGTLQLLK.ALPHLQINCSHFTTIARPTIDNQKNQE
Retrocopy PETLLELGEIPTL>KTLQVFGIVPDGTLQLLKKALPHLQINCSHFTTIARPTIDNQKNQE

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	1.00 RPM	6.23 RPM
SRP051959_heart	0.44 RPM	4.58 RPM
SRP051959_kidney	0.60 RPM	3.39 RPM
SRP051959_liver	0.54 RPM	5.63 RPM
SRP051959_lung	0.76 RPM	7.97 RPM
SRP051959_lymph_node	1.30 RPM	8.70 RPM
SRP051959_skeletal_muscle	0.31 RPM	2.40 RPM
SRP051959_spleen	0.95 RPM	6.47 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2367 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2367 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2367 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013562	4 retrocopies	retro_btau_1108, retro_btau_1612, retro_btau_525, retro_btau_555,
Choloepus hoffmanni	ENSCHOG00000006980	1 retrocopy	retro_chof_1604,
Callithrix jacchus	ENSCJAG00000018275	1 retrocopy	retro_cjac_2367 ,
Cavia porcellus	ENSCPOG00000013303	1 retrocopy	retro_cpor_1166,
Nomascus leucogenys	ENSNLEG00000016025	1 retrocopy	retro_nleu_2553,
Oryctolagus cuniculus	ENSOCUG00000009154	1 retrocopy	retro_ocun_158,
Pelodiscus sinensis	ENSPSIG00000008375	1 retrocopy	retro_psin_28,
Rattus norvegicus	ENSRNOG00000016823	1 retrocopy	retro_rnor_621,
Tupaia belangeri	ENSTBEG00000016814	1 retrocopy	retro_tbel_4354,