RetrogeneDB ID: retro_cjac_3821

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL284785.1:9435..10551(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAEA
• Ensembl ID: ENSCJAG00000001587
• Aliases: None
• Description: None

Sequence

>retro_cjac_3821
AAGGTGCCCTACGAGACAGTGAACAAACGCTTTCACGCCGCTCAGAAGAACACTGACAAGGAGACCAGCCACGTCACTAT
GGTGGTGGCCGAGCTGGAGAAGACGCTGAGTGTCTGCCCCGCCGTGGACTCTGTGGTCAGCCTGCTGGACGGTGTGGTGG
AGAAGCTCAGCATCCTTAAGAGGAAGGCGGCGGAGTCCATCCAGGCAGAGGATGAGAGCGCCAAGCTGTGCGAGAGCCGG
ATCGAGCACCTCAAAGAGCACAGCAGCGACCAGCCCTCGGTGTCCAGCGTGTGGAAGAGCAAGGACATGGACCGCATGGT
GGGGGAGCACCTGCTAAGCTGCGGCTACTACAACACGGCTGTCAAACTGGCACGCCAGAGCGGCATCAAGGACCTCGTGA
ATATCGAGATGTTCCTGACGGCCAAAGAGGTAGAGGAGTCCCTGGAGCGATGTGAGACAGCCACCTGCCTGGCCTGGTGC
CATGACAAGTCCTGGCTCTGGAAGATGAAGAGCTGCCTGGAGTTCAGCCTCAGAATCCAGGAGTTCATTGAACTCATCCG
GCAGAATAAGAGACTGGATGCCGTTAGACATGCGAGAAAGCACTTCACCCAAGTGGAAGGGAGCTAGCTGGACGAGGTGC
GCCAGGCCATGGGCATGCTGGCCTTCCTCCCTGACACGCACGTCTCCCCGTACAAGGACCTCCGGGACCCCGCACGGTGG
CGGATACTGATCCAGCAGTTCCGGTATGACAATACCGACTACACCAGCTGGGAAACAACTCCGTGTTCACCCTCACCCTG
CAGGCTGGCCTCTCCGCCATCAAGACACCACAGTACTACAAGGAGGACGGCAGCTCCAAGAGCCCCGACTGCCGTGTGCA
GCCGCTCCCTCAACAAGCTGGCGCAGCCCCTGCCCATGGCCCACTGCGCCAACTCCCGCCTGGACTACAAGATCTCCGGT
GATGTGATGAACCACAACAACCTGCCCATGATGCTGCCCAACGGCTACGTCTACGGCTACAATTCTCTGCTTTCTATCCG
TCAAGATGATAAAGTCATTTGCCCGAGAACCAAAGAAGTCTTTCACTTCTCATAAGCCGAGAAGGTGTACATCATG

Alignment

ORF - retro_cjac_3821 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.46 %
• Parental protein coverage: 99.73 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QVPYETLNKRFRAAQKNIDRETSHVTMVVAELEKTLSGCPAVDSVVSLLDGVVEKLSVLKRKAVESIQAE
          .VPYET.NKRF.AAQKN.D.ETSHVTMVVAELEKTLS.CPAVDSVVSLLDGVVEKLS.LKRKA.ESIQAE
Retrocopy KVPYETVNKRFHAAQKNTDKETSHVTMVVAELEKTLSVCPAVDSVVSLLDGVVEKLSILKRKAAESIQAE

Parental  DESAKLCKRRIEHLKEHSSDQPAAASVWKRKRMDRMMVEHLLRCGYYNTAVKLARQSGIEDLVNIEMFLT
          DESAKLC..RIEHLKEHSSDQP...SVWK.K.MDRM..EHLL.CGYYNTAVKLARQSGI.DLVNIEMFLT
Retrocopy DESAKLCESRIEHLKEHSSDQPSVSSVWKSKDMDRMVGEHLLSCGYYNTAVKLARQSGIKDLVNIEMFLT

Parental  AKEVEESLERRETATCLAWCHDNKSRLRKMKSCLEFSLRIQEFIELIRQNKRLDAVRHARKHFSQAEGSQ
          AKEVEESLER.ETATCLAWCHD.KS.L.KMKSCLEFSLRIQEFIELIRQNKRLDAVRHARKHF.Q.EGS.
Retrocopy AKEVEESLERCETATCLAWCHD-KSWLWKMKSCLEFSLRIQEFIELIRQNKRLDAVRHARKHFTQVEGS*

Parental  LDEVRQAMGMLAFPPDTHISPYKPCLSQVKSALTLQR-VEIRAFTLQRVDIRVKSALTLQRVDIRVKSAL
          LDEVRQAMGMLAF.PDTH.SPYK............Q..V......L..........LTLQ......K...
Retrocopy LDEVRQAMGMLAFLPDTHVSPYKDLRDPARWRILIQQ<VPV*QYRLHQLGNNSVFTLTLQAGLSAIKTP-

Parental  QCYKEDGSSKSPDC-PVCSRSLNKLAQPLP-MAHCANSRLVCKISGDVMNENNPPRMLPNGYVYGYNSLL
          Q.YKEDGSSKSPDC.P...........P.P.MAHCANSRL..KISGDVMN.NN.P.MLPNGYVYGYNSLL
Retrocopy QYYKEDGSSKSPDC<PCAAAPSTSWRSPCP<MAHCANSRLDYKISGDVMNHNNLPMMLPNGYVYGYNSLL

Parental  SIRQDDKVVCPRTKEVFHFSQAEKVYIM
          SIRQDDKV.CPRTKEVFHFS.AEKVYIM
Retrocopy SIRQDDKVICPRTKEVFHFS*AEKVYIM

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	0.31 RPM	4.90 RPM
SRP051959_heart	0.26 RPM	6.12 RPM
SRP051959_kidney	0.27 RPM	5.57 RPM
SRP051959_liver	0.32 RPM	3.36 RPM
SRP051959_lung	0.65 RPM	7.24 RPM
SRP051959_lymph_node	0.41 RPM	6.35 RPM
SRP051959_skeletal_muscle	0.24 RPM	4.06 RPM
SRP051959_spleen	0.44 RPM	5.80 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3821 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3821 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3821 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001587	2 retrocopies	retro_cjac_3821 , retro_cjac_567,