RetrogeneDB ID: retro_cjac_3340

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:114479494..114480797(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP2M1
• Ensembl ID: ENSCJAG00000012998
• Aliases: None
• Description: None

Sequence

>retro_cjac_3340
GTAATTGGAGGCTTATTCATCTATCATCACAAGGGGGAGGTGCTCATCTCCCGAGTCTACAGAGATGACATTTGGAGGAA
CACAGTAGATGCCTTTTGGGTCAATGTATCCATGCCCGGCAGCAGGTGCGCAGCCCCGTCACCAACATTGCACGCACCAG
CTTCCTTCACGTCAAGCGGTCCAACATCTGGCTGGCAGCAGTCACCAAGCAGAATGTCAACGCTGCCATGGTCTTCGAAT
TCCTCTATAAGATGTGTGATGTGATGGCTGCCTACTTCGGCAAGATCAGCGAGGAAAACATCAAGAACAATTTTGTTCTC
ATATATGAGCTGCTGGACGAGATTCTAGACTTTGGTTACCCACAGAATTCCGAGACAGGCGCGCTGAAAATCTTTATCAC
CCAGCAGGGCATCTAGAGTCAGCATCAGACAAAAGAAGAGCAGTCACAGATCACCAGCCAGGTGATGGGGCAGATCGGCT
GGCGGTGAGAGGGTATCAAGTATCTCCGGAATGAGCTCTTCCTGGACGTGCTGGAGAGTGTGAACCTGCTCACGTCCCCA
CAAGGGCAGGTGCTGAGCGCCCACGTGTCGGGCCGGGTGGTGATGAAGAGCGACCTGAGTGGGCTGCCTGAATGCAAATT
TGGGATGAATGACAAGATAGTCATTGAAAAACAGGGCAAAGGCACAGCTGATGAAACAAGCAAGAGCGGGAAGCAATCAG
TTGCCATTGATGACTGCACCTTCCACCAGTGTGTATGACTCAGCAAGTTTGACTCTGAAAGTAGCATCAGCTTCATCCCG
CCAGATGGAGAGTTTGCACTTATGAGGTAAGCACGACCAAGGACATCATCCTTCCTTTCCGGGTCATCCTACTAGTGCGA
GAAGTGGGACGCACCAAACTGGAGGTCAAGGTGATCATGAAGTCCAACTTTAAACCCTCATTGCTGGCTCAGAAGATTGA
GTTGAGGATCCCAACCACCCTGAACACAAGTGGGGTGCAGGTGATCTGCATGAAGGGGAAGGCCAAGTACATGGCCGGTG
AGAACACCATCGTATGGAAGATCAAGCGCATGGCAGGTAATAAGGAATCGCAGATCGGTGCAGAGATTGAGCTTCTGCCT
ACCAAATAGAAGAAGAAATGGGCTCGACCCCCCATTTCCATGAACTTCGAGGTGCCATTTGCACCCTCTGGCCTCAAGGT
GCGCTACTTGAAGGTGTTTGAACCGAAGCTGAACTACAGCGACCATGATGTCATCAAATGGGTGCGCTACATTGACCGCA
GCGGCATTTATGAAACTCGCTGC

Alignment

ORF - retro_cjac_3340 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.53 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNV-IHARQQVRSPVTNIARTSFFHVKRSNIWLAAVT
          .IGGLFIY.HKGEVLISRVYRDDI.RN.VDAF.VNV.IHARQQVRSPVTNIARTSF.HVKRSNIWLAAVT
Retrocopy VIGGLFIYHHKGEVLISRVYRDDIWRNTVDAFWVNV<IHARQQVRSPVTNIARTSFLHVKRSNIWLAAVT

Parental  KQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGYPQNSETGALKTFITQQGIK
          KQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGYPQNSETGALK.FITQQGI.
Retrocopy KQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGYPQNSETGALKIFITQQGI*

Parental  SQ--TKEEQSQITSQVTGQIGWRREGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGM
          SQ..TKEEQSQITSQV.GQIGWR.EGIKY.RNELFLDVLESVNLL.SPQGQVLSAHVSGRVVMKS.LSG.
Retrocopy SQHQTKEEQSQITSQVMGQIGWR*EGIKYLRNELFLDVLESVNLLTSPQGQVLSAHVSGRVVMKSDLSGL

Parental  PECKFGMNDKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMR-YR
          PECKFGMNDKIVIEKQGKGTADETSKSGKQS.AIDDCTFHQCV.LSKFDSE.SISFIPPDGEF.LMR...
Retrocopy PECKFGMNDKIVIEKQGKGTADETSKSGKQSVAIDDCTFHQCV*LSKFDSESSISFIPPDGEFALMR<VS

Parental  TTKDIILPFRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASE
          TTKDIILPFRVI.LVREVGRTKLEVKV..KSNFKPSLLAQKIE.RIPT.LNTSGVQVICMKGKAKY.A.E
Retrocopy TTKDIILPFRVILLVREVGRTKLEVKVIMKSNFKPSLLAQKIELRIPTTLNTSGVQVICMKGKAKYMAGE

Parental  NAIVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEPKLNYSDHDV
          N.IVWKIKRMAG.KESQI.AEIELLPT..KKKWARPPISMNFEVPFAPSGLKVRYLKVFEPKLNYSDHDV
Retrocopy NTIVWKIKRMAGNKESQIGAEIELLPTK*KKKWARPPISMNFEVPFAPSGLKVRYLKVFEPKLNYSDHDV

Parental  IKWVRYIGRSGIYETRC
          IKWVRYI.RSGIYETRC
Retrocopy IKWVRYIDRSGIYETRC

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	0.09 RPM	28.02 RPM
SRP051959_heart	0.05 RPM	36.57 RPM
SRP051959_kidney	0.13 RPM	42.09 RPM
SRP051959_liver	0.06 RPM	27.51 RPM
SRP051959_lung	0.07 RPM	33.56 RPM
SRP051959_lymph_node	0.05 RPM	27.33 RPM
SRP051959_skeletal_muscle	0.15 RPM	36.93 RPM
SRP051959_spleen	0.08 RPM	45.40 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3340 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3340 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3340 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012998	1 retrocopy	retro_cjac_3340 ,
Callithrix jacchus	ENSCJAG00000014070	3 retrocopies	retro_cjac_1985, retro_cjac_2135, retro_cjac_3873,
Erinaceus europaeus	ENSEEUG00000006073	1 retrocopy	retro_eeur_47,
Echinops telfairi	ENSETEG00000004759	1 retrocopy	retro_etel_2124,
Macropus eugenii	ENSMEUG00000002558	1 retrocopy	retro_meug_43,
Tarsius syrichta	ENSTSYG00000006101	1 retrocopy	retro_tsyr_1873,