RetrogeneDB ID: retro_cjac_287

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:68098254..68099103(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000021962
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SNRPA
• Ensembl ID: ENSCJAG00000014865
• Aliases: None
• Description: None

Sequence

>retro_cjac_287
ATGGCAGTTCCCGAGACCCGCCCTAACCACACTATTTATATCAACAACCTCAATGAGAAGATCAAGAAGGATGAGCTAAA
GAAGTCCCTGTACGCCATCTTCTCCCAGTTTGGGCAGATCCTGGATATCCTGGTGTCATGGAGCCTGAAGATGAGGGGCC
AGGCCTTTGTCATCTTCAAGGAGGTCAGCAGTGCCACCAACGCCCTGTGCTCCATGCAGGGCTTCCCCTTCTATGACAAG
CCCATGCGTATCCAGTATGCCAAGACCGACTCAGATATCATTGCCAAGATGAAAGGCACCTTTGTGGAGCGGGATCGCAA
GCGGGAGAAGAGAAAGCCCAAGAGCCAGGAGACACCAGCTGCCAAGAAGGCTGTGCAGGGCGGGGCAGCTGCCCCCGTGG
TGGGAGCTGTGCAGGGGCCTGTCCCGGGCATGCCACCAATGACTCAGGCACCGCGAATCATGCACCACATGCCAGGCCAG
CCACCCTACATGCCGCCCCCTGGCATGATCCCCCATCCAGGCCTTGCACCTGGCCAGATCCCACCAGGGGCCATGCCCCC
ACAGCAGCTCATGCCGGGACAGATGCCCCCTGCGCAGCCTCTTTCCGAGAATCCACCGAATCACATCTTGTTCCTCACCA
ACCTGCCAGAGGAGACCAACGAGCTCATGCTGTCCATGCTTTTCAATCAATTCCCTGGCTTCAAGGAGGTCCGTCTGGTC
CCCGGGCGGCATGACATCGCCTTCGTGGAGTTCGACAATGAGGTACAGGCAGGGGCAGCTCGCTATGCCCTGCAGGGCTT
TAAGATCACCCAGAACAACGCCATGAAGATCTCCTTTGCCAAGAAGTAG

Alignment

ORF - retro_cjac_287 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.86 %
• Parental protein coverage: 65.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PETRPNHTIYINNPQCKISTAELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQ
          PETRPNHTIYINN...KI...ELKKSLYAIFSQFGQILDILVS.SLKMRGQAFVIFKEVSSATNAL.SMQ
Retrocopy PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSWSLKMRGQAFVIFKEVSSATNALCSMQ

Parental  GFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPAAKKAVQGGAAAPVVGAVQGPVPP
          GFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPAAKKAVQGGAAAPVVGAVQGPVP.
Retrocopy GFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPAAKKAVQGGAAAPVVGAVQGPVPG

Parental  APQLSENP
          .P.....P
Retrocopy MPPMTQAP

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	1.42 RPM	2.26 RPM
SRP051959_heart	1.42 RPM	2.25 RPM
SRP051959_kidney	1.64 RPM	2.46 RPM
SRP051959_liver	2.10 RPM	3.57 RPM
SRP051959_lung	1.87 RPM	2.91 RPM
SRP051959_lymph_node	2.79 RPM	4.04 RPM
SRP051959_skeletal_muscle	0.94 RPM	1.46 RPM
SRP051959_spleen	2.12 RPM	3.19 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_287 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_287 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_287 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005091	1 retrocopy	retro_cfam_1114,
Callithrix jacchus	ENSCJAG00000004811	1 retrocopy	retro_cjac_269,
Callithrix jacchus	ENSCJAG00000014865	1 retrocopy	retro_cjac_287 ,
Cavia porcellus	ENSCPOG00000010875	1 retrocopy	retro_cpor_663,
Myotis lucifugus	ENSMLUG00000000219	1 retrocopy	retro_mluc_1517,
Monodelphis domestica	ENSMODG00000007912	1 retrocopy	retro_mdom_447,
Mustela putorius furo	ENSMPUG00000017681	1 retrocopy	retro_mputfur_593,
Mus musculus	ENSMUSG00000061479	6 retrocopies	retro_mmus_275, retro_mmus_3374, retro_mmus_469, retro_mmus_888, retro_mmus_889, retro_mmus_958,
Otolemur garnettii	ENSOGAG00000002864	1 retrocopy	retro_ogar_2046,
Pteropus vampyrus	ENSPVAG00000001494	1 retrocopy	retro_pvam_832,