RetrogeneDB ID: retro_cjac_193

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01199400.1:424..1753(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023239
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TEAD1
• Ensembl ID: ENSCJAG00000010263
• Aliases: None
• Description: None

Sequence

>retro_cjac_193
ACGGGCGCTCCTCCAAGCGGAGCCTTGGAGGGCAAGGCCGGCACCATTACCTCCAACGAGTGGAGCTCTCCCAACTCCCC
CGAGGGGAGCAACGTCTCTGGGAGCAGTCAGGCACTGGACAAGCCCATCGACAATGATGCAGAGGGCGTGTGGAGCCCGG
ACATCGAGCAGAGTTTCCAGGAGGCCCTGGCCATCTACCCGCCCTGCGGCTGGCGCAAAATCATCCTGTCAGACGAGGGC
AAGATGTACGGTCGAAACGAGCTGATTGCCCGCTACATCAAGCTCCGGACAGGGAAGACCTGCACCAGGAAGCAGGTCTC
CAGCCACATCCAGGTGCAGGCTCGTCGCAAAGCTCGCGAGATCCAGGCCAAGCTAAAGGACCAGGCAGCTAAGGACAAGG
CCCTGCAGAGCATGGCTGCCATGTCGTCTGCACAGATCATCTCCGCCACGGCCTTCCACAGTAGCATGGCCCTTGCCCGG
GGCCCTGGCTGCCCAGCAGTCTCAGGGTTTTGGCAAGGAGCTTTACCAGGCCAAGCCGGAACGTCCCATGATGTGAAGCC
TTTCTCTCAACAAACCTATGCTGTCCAGCATCCGCTGCCTCTGCCAGGCTTTGAGTCTCCTGCAGGGCCTGCCCCGTCGC
CCTCTGCACCCCCAGCACCCCCATGGCAGGGCCGCAGCGTGGCCAGCTCCAAACTCTGGATGTTGGAGTTCTCTGCCTTC
CTAGAGCAGCAGCAAGACCCGGACACGTACAACAAGCACCTGTTTGTGCACATTGGCCAGTCCAGCCCAAGCTATAGCGA
CCCCTACCTCGAAGCCGTAGACATCCGCCAGATCTATGACAAATTCCCTGAGAAGAAGGGTGGACTCAAGGAGCTCTTCG
AACGGGGACCCTCCAATGCCTTTTTTCTTGTGAAGTTCTGGGCAGACCTCAACACCAACATCGAGGATGAAGGCAGCTCC
TTCTACGGGGTCTCCAGCCAGTATGAAAGCCCTGAGAACATGATTATCACCTGCTCCACTAAGGTCTGCTCTTTCGGCAA
GCAGGTGGTGGAGAAGGTTGAGACAGAGTACGCTTGCTACGAGAATGGACACTACTCATACCGCATCCACCGGTCCCCGC
TCTGTGAGTACATGGTCAACTTCATCCACAAGCTGAAGCACCTGCCCGAGAAGTACATGATGAACAGCGTGCTGGAGAAC
TTCACCATCCTGCAGGTGGTCACCAACAGAGACACACAGGAGACCTTGCTATACATTGCCTATGTCTTTGAGGTGTCAGC
CAGCGAGCACGGGGCTCAGCACCATATCTACAGGCTGGTGAAAGAATGA

Alignment

ORF - retro_cjac_193 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.97 %
• Parental protein coverage: 99.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SDSADKPIDNDAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQ
          S...DKPIDNDAEGVWSPDIEQSFQEALAIYPPCG.RKIILSDEGKMYGRNELIARYIKLRTGKT.TRKQ
Retrocopy SQALDKPIDNDAEGVWSPDIEQSFQEALAIYPPCGWRKIILSDEGKMYGRNELIARYIKLRTGKTCTRKQ

Parental  VSSHIQVLARRKSRDFHSKLKDQTAKDKALQHMAAMSSAQIVSATAIHNKLGLPGIPRPTFPGAPGFWPG
          VSSHIQV.ARRK.R....KLKDQ.AKDKALQ.MAAMSSAQI.SATA.H....L.....P..P...GFW.G
Retrocopy VSSHIQVQARRKAREIQAKLKDQAAKDKALQSMAAMSSAQIISATAFHSSMALAR--GPGCPAVSGFWQG

Parental  MIQTGQPGSSQDVKPFVQQAYPIQPAVTAPIPGFE----PASAP-APSVPAWQGRSIGTTKLRLVEFSAF
          ....GQ.G.S.DVKPF.QQ.Y..Q.....P.PGFE....PA..P.AP..P.WQGRS....KL...EFSAF
Retrocopy ALP-GQAGTSHDVKPFSQQTYAVQHPL--PLPGFESPAGPAPSPSAPPAPPWQGRSVASSKLWMLEFSAF

Parental  LEQQRDPDSYNKHLFVHIGHANHSYSDPLLESVDIRQIYDKFPEKKGGLKELFGKGPQNAFFLVKFWADL
          LEQQ.DPD.YNKHLFVHIG....SYSDP.LE.VDIRQIYDKFPEKKGGLKELF..GP.NAFFLVKFWADL
Retrocopy LEQQQDPDTYNKHLFVHIGQSSPSYSDPYLEAVDIRQIYDKFPEKKGGLKELFERGPSNAFFLVKFWADL

Parental  NCNIQDDAGAFYGVTSQYESSENMTVTCSTKVCSFGKQVVEKVETEYARFENGRFVYRINRSPMCEYMIN
          N.NI.D....FYGV.SQYES.ENM..TCSTKVCSFGKQVVEKVETEYA..ENG...YRI.RSP.CEYM.N
Retrocopy NTNIEDEGSSFYGVSSQYESPENMIITCSTKVCSFGKQVVEKVETEYACYENGHYSYRIHRSPLCEYMVN

Parental  FIHKLKHLPEKYMMNSVLENFTILLVVTNRDTQETLLCMACVFEVSNSEHGAQHHIYRLVKD
          FIHKLKHLPEKYMMNSVLENFTIL.VVTNRDTQETLL..A.VFEVS.SEHGAQHHIYRLVK.
Retrocopy FIHKLKHLPEKYMMNSVLENFTILQVVTNRDTQETLLYIAYVFEVSASEHGAQHHIYRLVKE

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	0.29 RPM	17.93 RPM
SRP051959_heart	0.25 RPM	43.73 RPM
SRP051959_kidney	0.35 RPM	20.59 RPM
SRP051959_liver	0.13 RPM	3.99 RPM
SRP051959_lung	0.67 RPM	22.24 RPM
SRP051959_lymph_node	0.05 RPM	2.08 RPM
SRP051959_skeletal_muscle	1.09 RPM	45.88 RPM
SRP051959_spleen	0.08 RPM	4.83 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_193 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_193 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_193 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
Callithrix jacchus	ENSCJAG00000010263	1 retrocopy	retro_cjac_193 ,
Tupaia belangeri	ENSTBEG00000017462	1 retrocopy	retro_tbel_4523,
Tarsius syrichta	ENSTSYG00000001514	1 retrocopy	retro_tsyr_657,
Tursiops truncatus	ENSTTRG00000006621	1 retrocopy	retro_ttru_1096,