RetrogeneDB ID: retro_cjac_1145

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:44005831..44007227(-)
• Located in intron of: ENSCJAG00000005102

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMAD2
• Ensembl ID: ENSCJAG00000004630
• Aliases: None
• Description: None

Sequence

>retro_cjac_1145
ATGTCATCCATTTTGCCATTCACGCGGCCAGTTGTGAAGAGACTGCTGGGATAGAAGAAGTCAGCTGGTGCGTCTGGAGG
AGCAGGCGGAGGAGAGCAGAATGGGCAGGAAGAAAAGTGGTGTGAGAAAGCAGTGAAAAGTCTGGTGAAGAAGCTGAAGA
AAACAGGATGATTAGATGAGCTTGAGAAAGCCATCACCACTCAAAACTATAATACTAAACGTGTTACCATACCAAGCACT
TGCTCTGAAATCTTGGGACTGAGTACACCAAATATGATAGATCAGTGGGATACAACAGGCCTTTACAGCTTCTTAGAACA
AACCAGGTCTCTTGATGGTCGTCTCCAGGTATCCCATTGAAAAGGATTGCCACATGTTATTTATTGCCGATTATGGCGCT
GGCCTGATCTTCACAGTCATCATGAACTCAAGGCAATTAAAAACTGCGAATATGCTTTTAATCTTAAAAAGGATGAAGTA
TGTGTAAACCCTTACCACTATCAGAGAGTTGAAACACCAGTTTGGCCTCCAGTATTAGTGCCCTGACATACTGAGATCCT
AACAGAACTTCCGCCTCTGGATGACTGTACTCACTCCATTCCAGAAAACACTAACTTCCCGGCAGGAATTGAGCCACAGA
GTTATATTCCAGAAACGCTGCCTCCTAGATATATCAGTGAAGATGGAAAAACAAGTGCCAACAGTTGAATCAAAGTATGG
ACACAGGCTCTCCAGCAGAACTATCTCCTACTACTCTTTCCCCTGTTAATCATAGCTTGGATTTACAGCCAGTTACTTAC
TCAGAACCTGCATTTTGGTGTTCAATAGCATATTATGAATTAAATCAGAGGGTTGGAGAAACCTTCCATGCATCACAGCC
CTCACTCACTGTAGTTGGCTTTACAGACCCATCAAATTCAGAGAGGTTCTGCTTAGGTTTACTCTCCAATGTTAACCAAA
ATGCACAGTAGAAATGACAAGAAGGCACATAGGAAGAGGAGTGTACTTATATTACATAGGTAGGGAAGTCTTTGCTGAGT
GCCTAAGTGATAGTGCAATCTTTGTGCAGAGCCCCAATTGTAATCAGAGATATGGCTGGCACCCTGCAACGGTTTGTAAA
ATTCCACCAGGCTGTAATCTGAAGATCTTCAACAACCAGGAATTTGCTGCTCTTCTGGCTCAGTCTGTTAATCAGGGTTT
TGAAGCCGTCTATCAGCTAACTAGAATGTGCACCATAAGAATGAGTTTTGTGAAAGGGTGGGGAGCAGAATACCAAAGGC
AGATGGTAACAAGTACTCCTTGCTGGATTGAACTTCATCTGAATGGACTTCTGCAGTGGTTGGACAAAGTATTAACTCAG
ATGGGATCCCCTTCAGTGCGTTGCTCAAGCATGTCA

Alignment

ORF - retro_cjac_1145 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.03 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSSILPFTPPVVKRLLGWKKSAGGSGGAGGGEQNGQEEKWCEKAVKSLVKKLKKTGRLDELEKAITTQNC
          MSSILPFT.PVVKRLLG.KKSAG.SGGAGGGEQNGQEEKWCEKAVKSLVKKLKKTG.LDELEKAITTQN.
Retrocopy MSSILPFTRPVVKRLLG*KKSAGASGGAGGGEQNGQEEKWCEKAVKSLVKKLKKTG*LDELEKAITTQNY

Parental  NTKCVTIPSTCSEIWGLSTPNTIDQWDTTGLYSFSEQTRSLDGRLQVSHRKGLPHVIYCRLWRWPDLHSH
          NTK.VTIPSTCSEI.GLSTPN.IDQWDTTGLYSF.EQTRSLDGRLQVSH.KGLPHVIYCRLWRWPDLHSH
Retrocopy NTKRVTIPSTCSEILGLSTPNMIDQWDTTGLYSFLEQTRSLDGRLQVSH*KGLPHVIYCRLWRWPDLHSH

Parental  HELKAIENCEYAFNLKKDEVCVNPYHYQRVETPVLPPVLVPRHTEILTELPPLDDYTHSIPENTNFPAGI
          HELKAI.NCEYAFNLKKDEVCVNPYHYQRVETPV.PPVLVP.HTEILTELPPLDD.THSIPENTNFPAGI
Retrocopy HELKAIKNCEYAFNLKKDEVCVNPYHYQRVETPVWPPVLVP*HTEILTELPPLDDCTHSIPENTNFPAGI

Parental  EPQSNYIPETPPPGYISEDGETSD-QQLNQSMDTGSPAELSPTTLSPVNHSLDLQPVTYSEPAFWCSIAY
          EPQS.YIPET.PP.YISEDG.TS..QQLNQSMDTGSPAELSPTTLSPVNHSLDLQPVTYSEPAFWCSIAY
Retrocopy EPQS-YIPETLPPRYISEDGKTSA<QQLNQSMDTGSPAELSPTTLSPVNHSLDLQPVTYSEPAFWCSIAY

Parental  YELNQRVGETFHASQPSLTVDGFTDPSNSERFCLGLLSNVNRNA-TVEMTRRHIGRGVRLYYIGGEVFAE
          YELNQRVGETFHASQPSLTV.GFTDPSNSERFCLGLLSNVN.NA.TVEMTRRHIGRGV.LYYIG.EVFAE
Retrocopy YELNQRVGETFHASQPSLTVVGFTDPSNSERFCLGLLSNVNQNA<TVEMTRRHIGRGVYLYYIGREVFAE

Parental  CLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEFAALLAQSVNQGFEAVYQLTRMCTIRMSF
          CLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEFAALLAQSVNQGFEAVYQLTRMCTIRMSF
Retrocopy CLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEFAALLAQSVNQGFEAVYQLTRMCTIRMSF

Parental  VKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSVRCSSMS
          VKGWGAEY.RQ.VTSTPCWIELHLNG.LQWLDKVLTQMGSPSVRCSSMS
Retrocopy VKGWGAEYQRQMVTSTPCWIELHLNGLLQWLDKVLTQMGSPSVRCSSMS

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	1.04 RPM	28.89 RPM
SRP051959_heart	0.72 RPM	24.59 RPM
SRP051959_kidney	0.73 RPM	26.60 RPM
SRP051959_liver	0.41 RPM	18.45 RPM
SRP051959_lung	1.07 RPM	31.85 RPM
SRP051959_lymph_node	1.83 RPM	35.09 RPM
SRP051959_skeletal_muscle	0.44 RPM	19.30 RPM
SRP051959_spleen	1.47 RPM	33.80 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1145 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1145 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1145 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004630	1 retrocopy	retro_cjac_1145 ,
Pteropus vampyrus	ENSPVAG00000007760	1 retrocopy	retro_pvam_881,