RetrogeneDB ID: retro_cjac_1662

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:5954485..5955465(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC41
• Ensembl ID: ENSCJAG00000002860
• Aliases: None
• Description: coiled-coil domain containing 41 [Source:HGNC Symbol;Acc:17966]

Sequence

>retro_cjac_1662
ATGTTAATTGATGAAAGGTTACGATGTGGGCATCATAAAGCTAATTATCAGACTCTGAAAGCCGAACACACAAGGTTGCA
GAATGAATATGTAAAGTCACAAAATGAACTCAAGCACCTGTTAAATGAAAAGCAAATTCACCAGGAAAAACTTCAGCTGC
TTCAAGAACTAAGAGAAGAATTAGTAGAGAAAACTAAAGGCTTAGAAGAAATGAGACTGCAGATATTAACTCCACAAAAA
TTGGAATTGCTAAGAGCCCAAATTCAACAAGAATTAGAAACTCCAATGAGAGAACGTTTTCAGACCCCGGATGAAGAGGT
GGAAAAGTATAGAGCTGTATATAATAAGCTTCACTATGAACATACATTTCTCAAGTCAGAATTTGAACACCAGAAGGAAG
AGTTTGCGCATATTTTAGAATATGGAAAAATGAAATATCAATCAGAGACTGCAAGACTGGAGGAAGATAAAGAACTATGT
AACCAGCTGCTTAATGTTGATCTCACAAGAGACAGCAAACGAGTGAGCAACTTACTCGAGAAAAAGTCTATTTGTATAAA
AAATTAAAAGGTTTAGAGGCTGAAGTAGCAGAATTATGGGCTGAAAAGGAGAATTCTGGCACTCAGGTAGAAAATGTCCA
AAGAATACAGGTGCGGCAGTTGGCTGAGGTGCAGGCTACAGTCAGGTCCCCAGAGGCTGAAAAACAGTCAGCTAAGCTAT
GGGCAGAACACTTGGAAAAAGAGCTACAATCAAGCAATGAATAAAATACCTGTTTGATTAATAAATTGCATAAAGCAGAA
CAAGAAATAAATACATTGTCCAGTACAGTAAAAGAACTTAAACATCCAAACAAACTAGAAATAACAGACATCAAACTGGA
GGCAGCAAGAGCTAAGAGTGAGCTAGAAAAAGAAAGGAGTAAGATTCAAAGTGAACTGGATGGACTACGGTCAGACAATG
AAATTCTCAAAGCAGCTGTT

Alignment

ORF - retro_cjac_1662 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.24 %
• Parental protein coverage: 79.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLIDERLRCEHHKANYQTLKAEHTRIRLQNEYVKLQNELKHLLNEKQIHQEKLQLLLQELREELVEKTKD
          MLIDERLRC.HHKANYQTLKAEHTR..LQNEYVK.QNELKHLLNEKQIHQEKLQLL.QELREELVEKTK.
Retrocopy MLIDERLRCGHHKANYQTLKAEHTR--LQNEYVKSQNELKHLLNEKQIHQEKLQLL-QELREELVEKTKG

Parental  LEEMKLQILTPQKLELLRAQIQQELETPMRERFRTLDEEVEKYRAVYNKLRYEHTFLKSEFEHQKEEFAR
          LEEM.LQILTPQKLELLRAQIQQELETPMRERF.T.DEEVEKYRAVYNKL.YEHTFLKSEFEHQKEEFA.
Retrocopy LEEMRLQILTPQKLELLRAQIQQELETPMRERFQTPDEEVEKYRAVYNKLHYEHTFLKSEFEHQKEEFAH

Parental  VLEEGKIKYQSEIARLEEDKEELRNQLLNGDLTRDSKRV-EQLTREKVYLHQKLKGLEAEVAELRAEKEN
          .LE.GK.KYQSE.ARLEEDKE.L.NQLLN.DLTRDSKRV.EQLTREKVYL..KLKGL.............
Retrocopy ILEYGKMKYQSETARLEEDKE-LCNQLLNVDLTRDSKRV<EQLTREKVYLYKKLKGLXXXXXXXXXXXXX

Parental  SGAQVENVQRIQVRQLAEMQTTVRSLEAEKQSAKLRAEHLEKDLQSSNEQNTCLINKLHKAEREINSLSS
          ...QVENVQRIQVRQLAE.Q.TVRS.EAEKQSAKL.AEHLEK.LQSSNE.NTCLINKLHKAE.EIN.LSS
Retrocopy XXTQVENVQRIQVRQLAEVQATVRSPEAEKQSAKLWAEHLEKELQSSNE*NTCLINKLHKAEQEINTLSS

Parental  KVKELKHSNKLEITDIKLEAARAKSELEKERNKIQSELDGLQSDNEILKAAV
          .VKELKH.NKLEITDIKLEAARAKSELEKER.KIQSELDGL.SDNEILKAAV
Retrocopy TVKELKHPNKLEITDIKLEAARAKSELEKERSKIQSELDGLRSDNEILKAAV

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	0.75 RPM	17.51 RPM
SRP051959_heart	0.46 RPM	17.75 RPM
SRP051959_kidney	0.49 RPM	24.05 RPM
SRP051959_liver	0.43 RPM	18.28 RPM
SRP051959_lung	0.72 RPM	30.13 RPM
SRP051959_lymph_node	1.10 RPM	42.60 RPM
SRP051959_skeletal_muscle	0.26 RPM	11.31 RPM
SRP051959_spleen	0.46 RPM	31.41 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1662 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1662 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1662 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009750	1 retrocopy	retro_amel_1376,
Callithrix jacchus	ENSCJAG00000002860	1 retrocopy	retro_cjac_1662 ,
Cavia porcellus	ENSCPOG00000008997	1 retrocopy	retro_cpor_1537,
Rattus norvegicus	ENSRNOG00000007859	1 retrocopy	retro_rnor_384,