RetrogeneDB ID: retro_cjac_3115

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:15971287..15972010(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GDI2
• Ensembl ID: ENSCJAG00000020512
• Aliases: None
• Description: None

Sequence

>retro_cjac_3115
GTGACTAAAGGGAGCTTTGTCTATAAGGGTGGACAAATCTACAAGGGTTCTTCCACTGAGGCAGAAGCCTGGCATCTAGC
TTAATGGGACGGTTTAAAAAATGTCACTTTGGGAAATCCCTAGTGTATGTTGCCAACATAGATGGAAAAGATCCGAGAAC
TTTTGAGGGAATTGATCCTAAGAAAACCCAACGTGAGAGGCGTATAAGAAATTTGATTTGGGCCAAGATGTTACGGATTT
TACTGGTCATGCTCTTGCGCTTTACAGAAGTGATGACCAGTTAGATTAACCATGTTGTGAAACCATTAATGGAATTAAAC
ATGACAGAGAATCTTTTCAACATACGGCAAAAGTCCATCCCTTTACCCACTCTAAGGCCTTGGAGAACTGTCACACAGCT
GTTTGCAAGGCTAAGTGCTATTTATGAGGTACCCAAGGTCAAATAAACCGATTGAATAAATCATTTTGCAGAATGGAAAA
GTAATTGGTGTAAAATCCGAAGGAGAAGTTGCTTGCTGTAAGCAGCTCATCTGTGACCCCAGCTACATAAAAGACTGGCT
AGAAAGAGTGGACCAGGTAATCAGAGTTACTTGGATCCTCAGCCACCCCATCAAGAACGCCAGTGATGTCAACTCCTGTC
AGGTCATTATTCCAAAGAACCAAGTCAGTCAAAAGTCAGATATCTGGATTTGCACAATCTCCTCCATGCACAGTGTAGCG
GCA

Alignment

ORF - retro_cjac_3115 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.2 %
• Parental protein coverage: 54.38 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VTEGSFVYKGGKIYKVPSTEAEA-LASSLMGLFEKRRFRKFLVYVANFDEKDPRTFEGIDPMKTTMR-EV
          VT.GSFVYKGG.IYK..STEAEA.LASSLMG.F.K..F.K.LVYVAN.D.KDPRTFEGIDP.KT....E.
Retrocopy VTKGSFVYKGGQIYKGSSTEAEA<LASSLMGRFKKCHFGKSLVYVANIDGKDPRTFEGIDPKKTQRE<EA

Parental  YKKFDLGQDVIDFTGHALALYRTDDYLDQPCCETINRIKLYSESL-ARYGKSPYLYPLYGLGELPQGFAR
          YKKFDLGQDV.DFTGHALALYR.DD.LD.PCCETIN.IK...ES....YGKSP.LYPL.GLGEL......
Retrocopy YKKFDLGQDVTDFTGHALALYRSDDQLD*PCCETINGIKHDRESF<STYGKSPSLYPL*GLGELSHSCLQ

Parental  LSAIYGGTYMLNKPIEEIIVQNGKVIGVKSEGEIARCKQLICDPSYVKDRVEKVGQVIRVICILSHPIKN
          ...........NKPIE.II.QNGKVIGVKSEGE.A.CKQLICDPSY.KD..E.V.QVIRV..ILSHPIKN
Retrocopy G*VLFMRYPRSNKPIE*IILQNGKVIGVKSEGEVACCKQLICDPSYIKDWLERVDQVIRVTWILSHPIKN

Parental  TNDANSCQIIIPQNQVNRKSDIYVCMISSAHNVAA
          ..D.NSCQ.IIP.NQV..KSDI..C.ISS.H.VAA
Retrocopy ASDVNSCQVIIPKNQVSQKSDIWICTISSMHSVAA

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	0.00 RPM	95.32 RPM
SRP051959_heart	0.00 RPM	57.76 RPM
SRP051959_kidney	0.00 RPM	82.95 RPM
SRP051959_liver	0.00 RPM	111.51 RPM
SRP051959_lung	0.00 RPM	71.69 RPM
SRP051959_lymph_node	0.00 RPM	84.91 RPM
SRP051959_skeletal_muscle	0.00 RPM	36.51 RPM
SRP051959_spleen	0.00 RPM	105.53 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3115 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3115 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3115 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005316	1 retrocopy	retro_btau_1208,
Canis familiaris	ENSCAFG00000005223	2 retrocopies	retro_cfam_2196, retro_cfam_886,
Callithrix jacchus	ENSCJAG00000020512	2 retrocopies	retro_cjac_1168, retro_cjac_3115 ,
Cavia porcellus	ENSCPOG00000013449	1 retrocopy	retro_cpor_696,
Gorilla gorilla	ENSGGOG00000003623	1 retrocopy	retro_ggor_2590,
Mus musculus	ENSMUSG00000021218	2 retrocopies	retro_mmus_2971, retro_mmus_360,
Oryctolagus cuniculus	ENSOCUG00000005367	1 retrocopy	retro_ocun_69,
Ictidomys tridecemlineatus	ENSSTOG00000006449	1 retrocopy	retro_itri_757,
Tupaia belangeri	ENSTBEG00000011523	1 retrocopy	retro_tbel_644,