RetrogeneDB ID: retro_cjac_511

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:26791140..26793063(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSRP2BP
• Ensembl ID: ENSCJAG00000005057
• Aliases: None
• Description: None

Sequence

>retro_cjac_511
ATGGAGAGTAGCATCCACCTGAGTAGTCTGATTAGTCGGCACGGTGACGAAGCCACGAGAACACCGACCTCAGAAGGACT
GGAGGAAGGTGAAGTGGAGGGAGAGTCGCTCCTGATTGTGGAATCTGAGGATCAGGCTCAGTGGATTATCACACGACCAG
AGTGGGGATTCCCTCAACAGTGATGAAGGAGGCGTGTCGTGGATGGAGGAGCAGCTGCCCTACTTCTGTGACAAGTGCCA
AAAACGGATACCAGCCACTCAGCTGAGGGAACAGCTCAGTTACCTTAAGGGTGATAATTTTTTAGGCTTACTTGTTCAGA
TTGCTCAGCAGATGGCAAGGAGCAGCATGAAAGGCTGAAGCTGACATGGCAGCAGGTCGTCATGTTGGCGATGGACAACT
TGTCTCTAGAAGGAAGTGGACGTCAAGGTTATTTCAGGTGGAAAGAAGACATCTGCGCTTTTATTGAGAAGCATTGGACT
TTTTTACTAGGGAATAGGAAAAAGACGTCCACCTGGTGAAGCACTGTGTCAGGGTGCCTCAGCGTGGGAAGTCCCACGTA
TTTCCATTCAGGTGCTCAGGATTTGGAGAGTCGGGATGGTGCAAACTTGTTCATAACAAGCCCCAACAATGAGACCTGAA
GGAGAGAAGCTGTCTGCCTTGATTTTGAAAATACAAGTAGCCTCGAAACCAACTTTAGATCCCTTCATGACTGTCGAGGG
ACTTAGAAAAGGGGCAAGTCGGAATCCTGTAGAATCTGCCACGGAATTACAAGAGAAAAGGTCTCGAACTCAGGAAGCAA
AAGACGTTAGAAGAGCCCAAAAGGAGGCGGCTGCTTTCCTGACAGGAGCACGTCTTCTACCCCTGTAATGTTCATAAAAC
AAGGCCATAGGCCGGATGTGATTCTTGAAAAGGGAGAACTGATTGACTTTTCCTCCTTCAGCTCCTCTGACTGCACCCCG
CAGACAAGCCCATCTCCTTCTCTGGATTGCTCTGCCCCTGGGACACCTGCCTCTCATTCTGCCATGCCTAGCTTGCTTTC
AGAAGCAGATCTGATTCCAGATGTGATGCCCCCGCAAGCCTTGTTTCACGATGATGCTTAGATGGAAAGTGATGGAGTCA
TAGACCCAGGGATGGAGAACATTCCACCCCCTTCTGGGTCAGTGGCTTCTGGGCCAGTGGTTGGGGGCAGAAAGAAGGTC
AGAGGCCCTGAACAGATAAAGCAGGAGGTAGAGAGTGAGGAAGAAAAACCCGACAGGATGGATATTGACAGTGAAGACAC
AGATTCCAACCCATCTTTGCAAACAAGGGCTTGAGAAAAGAGGAAGCCTCAGCTGGAGAAGGACACAAAGGCGAAAGAGC
CCAAATATACTCCCATGAGCATCAGTGAGGAAAAGCTGTTGCCCAAGAGGCTGGAAGCTTGTCCCGGTGCGGTTGCCATG
ACTCCGGAAGCTCGGAGACTGAAGCGCAACCTGATTGTCAGACAAGCGAAAAGGGATAGGGGATTACCACTTTTTGACTT
GGATCAATTTGTTAATGCTGCTCTTCTTTTAGTTGATGGGATTTATGGAGCCAAAGACGGAGGAGTTTCCAGACTTTCAG
CTGGACAAGCCATGTACCGAACTACCTGTCAGGACTTCAGAATCCTTGACCGATACCAGACGTCCTTGGAAGGGATTTCA
ACACCAGACTACCAAGTTTTGTATCGCTTGGTAGGATCAGAAGATATGGCTGTGGACCAGACTATTGTCAGCCCTTATAC
CTCTCGGATCTTGAAACCTTATATCAGGCGTGATTGTGAAACAAAGCCACCCAAACTGCAGCTCCTATCACAGATTCGTT
CCCACCTGCACAGGAGCAACCCTCGCTGGATGCCGGAGCCCGATGCACCTCTTGATTACTGTTATATGCAGCCATATCAT
ATC

Alignment

ORF - retro_cjac_511 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.28 %
• Parental protein coverage: 82.95 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MESSIHLSSLISRHDDEATRTSTSEGLEEGEVEGETLLIVESEDQA-SVD-LSHDQSGDSLNSDEGDVSW
          MESSIHLSSLISRH.DEATRT.TSEGLEEGEVEGE.LLIVESEDQA.SVD.LSHDQSGDSLNSDEG.VSW
Retrocopy MESSIHLSSLISRHGDEATRTPTSEGLEEGEVEGESLLIVESEDQA<SVD<LSHDQSGDSLNSDEGGVSW

Parental  IEEQLSYFCDKCQKWIPASQLREQLSYLKGDNF-FRFTCSDCSADGKEQYERLKLTWQQVVMLAMYNLSL
          .EEQL.YFCDKCQK.IPA.QLREQLSYLKGDNF.FR.TCSDCSADGKEQ.ERLKLTWQQVVMLAM.NLSL
Retrocopy MEEQLPYFCDKCQKRIPATQLREQLSYLKGDNF<FRLTCSDCSADGKEQHERLKLTWQQVVMLAMDNLSL

Parental  EGSGRQGYFRWKEDICAFIEKHWTFLLGNRKKTSTWWSTVAGCLSVGSPMYFRSGAQE-FGESGWWKLVH
          EGSGRQGYFRWKEDICAFIEKHWTFLLGNRKKTSTW.STV.GCLSVGSP.YF.SGAQ..FGESGW.KLVH
Retrocopy EGSGRQGYFRWKEDICAFIEKHWTFLLGNRKKTSTW*STVSGCLSVGSPTYFHSGAQD<FGESGWCKLVH

Parental  NKP-PTMKPEGEKLSASTLKIKDSFLAASKPTLDPIITVEGLRKRASRNPVESAMELKEKRSRTQEAKDI
          NKP.PTM.PEGEKLSA..LKI......ASKPTLDP..TVEGLRK.ASRNPVESA.EL.EKRSRTQEAKD.
Retrocopy NKP<PTMRPEGEKLSALILKIQ----VASKPTLDPFMTVEGLRKGASRNPVESATELQEKRSRTQEAKDV

Parental  RRAQKEAAGFL-DRSTSSTPVKFISRGRRPDVILEKGEVIDFSSLSSSDRTPLTSPSPSPSLDFSAPGTP
          RRAQKEAA.FL.DRSTSSTPV.FI..G.RPDVILEKGE.IDFSS.SSSD.TP.TSPSPS..LD.SAPGTP
Retrocopy RRAQKEAAAFL<DRSTSSTPVMFIKQGHRPDVILEKGELIDFSSFSSSDCTPQTSPSPS--LDCSAPGTP

Parental  ASHSATPSLLSEADLIPDVMPPQALFHDDDEMEGDGVIDPGMEYIPPPSGSVASGPVVGSRKKVRGPEQI
          ASHSA.PSLLSEADLIPDVMPPQALFHDD..ME.DGVIDPGME.IPP...........G.RKKVRGPEQI
Retrocopy ASHSAMPSLLSEADLIPDVMPPQALFHDDA*MESDGVIDPGMENIPPXXXXXXXXXXXGGRKKVRGPEQI

Parental  KQEVESEEEKPDRMDIDSEDTDSNTSLQTRAREKRKPQLEKDTKPKEPKYTPVSIYEEKLLLKRLEACPG
          KQEVESEEEKPDRMDIDSEDTDSN.SLQTRA.EKRKPQLEKDTK.KEPKYTP.SI.EEKLL.KRLEACPG
Retrocopy KQEVESEEEKPDRMDIDSEDTDSNPSLQTRA*EKRKPQLEKDTKAKEPKYTPMSISEEKLLPKRLEACPG

Parental  AVAMTPEARRLKRKLIVRQAKRDRGLPLFDLDQVVNAALLLVDGIYGAKE-GVSRLSAGQAMYRTTCQDF
          AVAMTPEARRLKR.LIVRQAKRDRGLPLFDLDQ.VNAALLLVDGIYGAK..GVSRLSAGQAMYRTTCQDF
Retrocopy AVAMTPEARRLKRNLIVRQAKRDRGLPLFDLDQFVNAALLLVDGIYGAKDGGVSRLSAGQAMYRTTCQDF

Parental  RILDRYQTSLPSRKGFRHQTTKFLYRLVGSEDMAVDQSIVSPYTSRILKPYIRRRDYETKPPKLQLLSQI
          RILDRYQTSL....G........LYRLVGSEDMAVDQ.IVSPYTSRILKPYI.RRD.ETKPPKLQLLSQI
Retrocopy RILDRYQTSL---EGISTPDYQVLYRLVGSEDMAVDQTIVSPYTSRILKPYI-RRDCETKPPKLQLLSQI

Parental  RSHLHRSDPRWTPEPDAPLDYCYVRPNHI
          RSHLHRS.PRW.PEPDAPLDYCY..P.HI
Retrocopy RSHLHRSNPRWMPEPDAPLDYCYMQPYHI

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	0.71 RPM	11.47 RPM
SRP051959_heart	0.28 RPM	10.47 RPM
SRP051959_kidney	0.24 RPM	14.35 RPM
SRP051959_liver	0.02 RPM	9.29 RPM
SRP051959_lung	0.20 RPM	14.17 RPM
SRP051959_lymph_node	0.21 RPM	13.20 RPM
SRP051959_skeletal_muscle	0.24 RPM	15.42 RPM
SRP051959_spleen	0.23 RPM	14.01 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_511 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_511 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_511 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005057	1 retrocopy	retro_cjac_511 ,
Dasypus novemcinctus	ENSDNOG00000008372	1 retrocopy	retro_dnov_2414,