RetrogeneDB ID: retro_cjac_2198

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:165317123..165318117(+)
• Located in intron of: ENSCJAG00000021061

Retrocopy information

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

Parental gene information

• Parental gene symbol: SH3GLB2
• Ensembl ID: ENSCJAG00000020282
• Aliases: None
• Description: None

Sequence

>retro_cjac_2198
ATGGACTTCAACATGAAGAAGCTGGCGTCGGACGCGGGCACCTTTTATCCCGGGCCGTGCAGTTCATTGAGTAGAAGTGT
GGCCAGGCTGAGAAGACCGAGCTTGATGCCCACTTTGAAAACCTTCTGGCCCGGCCAGACAGCACCAAGAACTGGACAGA
GAAGATCCTGAGGCAGACAGAAGTGCTGCTGCAGCCCAACCCTACTGCCCGGGTGGCAGAGTTCCTGTATGAGAAGCTGG
ACAGGAAGGTCCCCTCACGGGTCACCAACGGAGAGCTGCTGGCACAGTACATGGCAGAGGCGGCCAGTGAGCTGGGGCCC
ACCACCCTCTGTGGGAAGACACTGCTCAAGGTGGCATAAGCTGAAAAGCAGCTGGGAGTCGCGGAGAGGGATTTTATCCA
CACAGCCTCCATCGGCTTCCTCACACCCCTGCGCAACTTCCTGGAGGGGGCCTGGAAGACCGTCTCGAAGGAGAGGCGGC
TCCTCCAAAACCGGCGTCTGGATTGGATGCCTGCAAAGCGAGGCTGAAGAAGGCCAAGGCCGCAGAAGCCAAAGCCACGA
CGGTGCCTGGCTTTCAGGAGACTAGATTTCGTAATTACATTTTCTCAGCCAGCACCTCCGCGCTCTGGAACGATGAGGTG
GACAAGGCTGAGCAGGAGCTCCGTGTGGCCCAGACAGAGTTTGACCGGCAAGCAAAAGTGACCCTTCTCTTGCTGGAGGG
AATCAGCAGCACTCACGTGAACCACCTGCGCTGCCTCCATGGATTTGTCAAGTCTCAGACAACCTGCTAGGCGCAGTGCT
ACCGCCACATGCTGGACTTGCAGAAGCAGCTGGGCAGATTTCCAGGCACCTTCCTGGGCACCACAGAGCCCGCCTCGCCA
CCCCTGAGCAGCACCTCACCCACCACTGCTGCAGCCACTATGCCTGTGGTGCTCTCGGTGGCCAGCCTGGCCCCTTTGGG
GGAGGCCTCGCTCTGCCTGGAAGAGGTGCCCCCA

Alignment

ORF - retro_cjac_2198 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.82 %
• Parental protein coverage: 84.05 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDFNMKKLASDAGIFF-TRAVQFTEEKFGQAEKTELDAHFENLLARADSTKNWTEKILRQTEVLLQPNPX
          MDFNMKKLASDAG.F...RAVQF.E.K.GQAEKTELDAHFENLLAR.DSTKNWTEKILRQTEVLLQPNP.
Retrocopy MDFNMKKLASDAGTFY<SRAVQFIE*KCGQAEKTELDAHFENLLARPDSTKNWTEKILRQTEVLLQPNPT

Parental  ARVEEFLYEKLDRKVPSRVTNGELLAQYMAEAASELGPTTPYGKTLLKVAEAEKQLGATERDFIHTASIS
          ARV.EFLYEKLDRKVPSRVTNGELLAQYMAEAASELGPTT..GKTLLKVA.AEKQLG..ERDFIHTASI.
Retrocopy ARVAEFLYEKLDRKVPSRVTNGELLAQYMAEAASELGPTTLCGKTLLKVA*AEKQLGVAERDFIHTASIG

Parental  FLTPLRNFLEGDWKTISKERRLLQNRRLD-LDACKARLKKAKAAEAKATTVPDFQETRPRNYILSASASA
          FLTPLRNFLEG.WKT.SKERRLLQNRRLD.LDACKARLKKAKAAEAKATTVP.FQETR.RNYI.SAS.SA
Retrocopy FLTPLRNFLEGAWKTVSKERRLLQNRRLD<LDACKARLKKAKAAEAKATTVPGFQETRFRNYIFSASTSA

Parental  LWNDEVDKAEQELRVAQTEFDRQAEVTRLLLEGISSTHVNHLRCLHEFVKSQTTYYAQCYRHMLDLQKQL
          LWNDEVDKAEQELRVAQTEFDRQA.VT.LLLEGISSTHVNHLRCLH.FVKSQTT..AQCYRHMLDLQKQL
Retrocopy LWNDEVDKAEQELRVAQTEFDRQAKVTLLLLEGISSTHVNHLRCLHGFVKSQTTC*AQCYRHMLDLQKQL

Parental  GRFPGTFVGTTEPTSPPLSSTSPTTTAATMPVVPSVASLAPPGEASLCLEEVAP
          GRFPGTF.GTTEP.SPPLSSTSPTT.AATMPVV.SVASLAP.GEASLCLEEV.P
Retrocopy GRFPGTFLGTTEPASPPLSSTSPTTAAATMPVVLSVASLAPLGEASLCLEEVPP

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	0.44 RPM	6.30 RPM
SRP051959_heart	0.47 RPM	6.72 RPM
SRP051959_kidney	0.84 RPM	14.62 RPM
SRP051959_liver	0.32 RPM	5.94 RPM
SRP051959_lung	0.20 RPM	6.56 RPM
SRP051959_lymph_node	0.43 RPM	8.95 RPM
SRP051959_skeletal_muscle	0.15 RPM	4.02 RPM
SRP051959_spleen	0.32 RPM	4.37 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2198 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2198 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2198 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	ENSCJAG00000020282	1 retrocopy	retro_cjac_2198 ,
Equus caballus	ENSECAG00000004437	1 retrocopy	retro_ecab_1079,