RetrogeneDB ID: retro_cjac_475

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:153002549..153004003(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000017296
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ZYG11A
• Ensembl ID: ENSCJAG00000004369
• Aliases: None
• Description: None

Sequence

>retro_cjac_475
GACTCAACAAGCATCTCTCAAAATTCAAGAGTACTGTTCTTTGGTCAGCTCACTGGTCTTTGCATTTTAAGTGTTTTTAA
TGTTTGTTTTCATACTGAAGACCTGGCTAATGTTTCTCAGTTACCAAGACTGGAAAGCTTGGGTATCTCTAGTACTCTGG
TCACGGATATTTCTGCACTGCTTACCTGTAAGGATCGATTGAAGCCTCTCACAATGCACTATCTGAAATGCCTGACCATG
ACCAAACCACAAATTCTTGCAGTCATTAGAGAACTTAAATGTCTGCTTCACCTTGACATTTCTGATCACAAGCAACTCAA
ATCAGACCTAGCTTTTCATTTGCTACAGCAGAAGGATATCCTGCCCAATGTCGTGTCACTGGGTATTTCTGGGAGCAATT
GCATCACTGATGCAGCTGTAGAACTGTTTATGCGACAGTGGCCTGCCATGCAATTTGTGGGACTATTGGCCACAGATGCT
GGCTATTCTGACTTCTTTACTACAAAGCAAGGCTTGAGGGTTGCTGGAGGAGTCAATATGAGTCAGATTTCAGAAGCACT
GAGCCGATACAGGAACAGATCATGTTTTATGAAGGAAGCCCTCTACAGGCTATTCACAGAGACATTGTCAATGAAGGTAA
CCATGCCTGCTATTTTAAAGCTTGTGACTGTAGGAATGAGGAATCACCGTTGGATTTGCCAGTGCAATTCACAGCTAGTG
CTTGCGCTCTCAACCTAACACACCACGGCCTGGCCAAGGGGATGCCTGTTCGCCTGTTGTCAGAGGTCACCTGTCTACTT
TTCAAGGCTCTGAAAAATTTCCCTTGTTACCAACAGTTACAGAAGAATTGTCTTCTCTCCTTAACCAATTCCAGGATTCT
TGTGGATGTTCTGTTTGACAGGTTTGGTGCTGCCAAGTTTGTTATGAGATGGCTCAGTAAGCATGAAAACCCCAAGATGA
AAACAATAGCAGCGAGTGTCACCTCTATTCTAGCTCTGCAGCTTTCACCTCAGCAAACGGCAGAGCTTGAAGAGCTTTTC
ATGGCAGTTAAGGAACTTCTAGCAATAGTAAAACAAAAGACTACTGAGAATTTAGATGATGTCACCCTCTTGTTTACTTC
AAAAGCACTTTGGAATCTTACAGACGAGTCTCCAGCTGCCTGCAAGCACTTTATTGAAAATCAAGGATTGGAAATCTTCA
TCCAAGTCTTGGAGACCTTTTCAAAGTCAGCAATACAAAGCAAAGTACTTGGTCTTTTGAACAACATAGCAGAAGTCAGA
GAGCCTTCTGCCAAGCTGGTGACTGAAGACGTGCTGAAGCATATCAACAATTTACTCTGTAGCAGGGAAATGGAAGTCAG
CTATTTTGCTGCAGGTATCATAGCCCACCTGACATCTGACAGACAACTTTGGATATCCCATGACTTCCAGAGGCATTTTC
TTCTGCAAGATCTG

Alignment

ORF - retro_cjac_475 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.21 %
• Parental protein coverage: 71.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DSTSISQNSRVLFFGQLTGLCVLSVFNVCFHTEDLANVSQLPRLESLDISSTLVTDISALLTCKDRLKSL
          DSTSISQNSRVLFFGQLTGLC.LSVFNVCFHTEDLANVSQLPRLESL.ISSTLVTDISALLTCKDRLK.L
Retrocopy DSTSISQNSRVLFFGQLTGLCILSVFNVCFHTEDLANVSQLPRLESLGISSTLVTDISALLTCKDRLKPL

Parental  TMHYLKCLTMTKPQILAVIRQLKCLLHLDISDHKQLKSHLAFHLLQQKDILPNIVSLDISGSNCITDAAV
          TMHYLKCLTMTKPQILAVIR.LKCLLHLDISDHKQLKS.LAFHLLQQKDILPN.VSL.ISGSNCITDAAV
Retrocopy TMHYLKCLTMTKPQILAVIRELKCLLHLDISDHKQLKSDLAFHLLQQKDILPNVVSLGISGSNCITDAAV

Parental  ELFIRQRPAMQFVGLLATDAGYSDFFTTKQGLRVAGGANMSQISEALSRYRNRSCFMKEALYRLFTETLS
          ELF.RQ.PAMQFVGLLATDAGYSDFFTTKQGLRVAGG.NMSQISEALSRYRNRSCFMKEALYRLFTETLS
Retrocopy ELFMRQWPAMQFVGLLATDAGYSDFFTTKQGLRVAGGVNMSQISEALSRYRNRSCFMKEALYRLFTETLS

Parental  MKVTMPAILKLVTVGMRNH-PLDLPVQFTASACALNLTRHGLAKGMPVRLLSEVTCLLFKALKNFPHYQQ
          MKVTMPAILKLVTVGMRNH.PLDLPVQFTASACALNLT.HGLAKGMPVRLLSEVTCLLFKALKNFP.YQQ
Retrocopy MKVTMPAILKLVTVGMRNH<PLDLPVQFTASACALNLTHHGLAKGMPVRLLSEVTCLLFKALKNFPCYQQ

Parental  LQKNCLLSLTNSRILVDVPFDRFDAARFVMRWLCKHENPKMQTMAVSVTSILALQLSPQQTAHLEELFMA
          LQKNCLLSLTNSRILVDV.FDRF.AA.FVMRWL.KHENPKM.T.A.SVTSILALQLSPQQTA.LEELFMA
Retrocopy LQKNCLLSLTNSRILVDVLFDRFGAAKFVMRWLSKHENPKMKTIAASVTSILALQLSPQQTAELEELFMA

Parental  VKELLAIVKQKTTENLDDVTLLFTLKALWNLTDESPAACKHFIENQGLEIVIQVLETFSESAIQSKVLGL
          VKELLAIVKQKTTENLDDVTLLFT.KALWNLTDESPAACKHFIENQGLEI.IQVLETFS.SAIQSKVLGL
Retrocopy VKELLAIVKQKTTENLDDVTLLFTSKALWNLTDESPAACKHFIENQGLEIFIQVLETFSKSAIQSKVLGL

Parental  LNNIAEVRELSSKLVTEDVLKHINSLLWSREMEVSYFAAGIIAHLTSDRWLWISRDVQRRILLQDL
          LNNIAEVRE.S.KLVTEDVLKHIN.LL.SREMEVSYFAAGIIAHLTSDR.LWIS.D.QR..LLQDL
Retrocopy LNNIAEVREPSAKLVTEDVLKHINNLLCSREMEVSYFAAGIIAHLTSDRQLWISHDFQRHFLLQDL

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	0.04 RPM	0.18 RPM
SRP051959_heart	0.00 RPM	0.46 RPM
SRP051959_kidney	0.27 RPM	3.99 RPM
SRP051959_liver	0.04 RPM	0.41 RPM
SRP051959_lung	0.08 RPM	1.09 RPM
SRP051959_lymph_node	0.00 RPM	0.23 RPM
SRP051959_skeletal_muscle	0.02 RPM	0.28 RPM
SRP051959_spleen	0.00 RPM	0.32 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_475 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_475 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_475 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004369	1 retrocopy	retro_cjac_475 ,