RetrogeneDB ID: retro_cjac_2131

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:41577545..41578429(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000002277
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SRM
• Ensembl ID: ENSCJAG00000002354
• Aliases: None
• Description: spermidine synthase [Source:HGNC Symbol;Acc:11296]

Sequence

>retro_cjac_2131
GGCCCTGCCGCCTCCGCCCCACTGCTATCCGCAAGGGCTGGTTCCGCGAGACCTGCAGCCGGTGGCCCGGCCAGGCCCTG
TCGCTGCAGGTGAAGCAGCTGCTCCACCACCGGCACTCGTGCTACCAGAACATCCTCGTTTTCCACAGTAAGACCTATGG
CAACATGCTGGTGTTGGACGGTGTCATCCAGTGCACAGAGAGGGATGAGTTCTCCTACCAGGAGATGATCGCCAACCTGC
CTCTCTGCAGCCACCCCAACCCGCAAAAGGTGCTAATCATCGGGGGTGGAGACAGAGGTGTCCTGTGCGAGGTGGTGAAG
CACCCCTCGGTGGAGTCCGTGGTTCATTGTGAGATCGACGAGGATGTCATCCAAGTCTCCAAGAAGTTCCTGCCGGGAAT
GGCTGTTGGCTATTCTAGCTCGAAGCTGACCCTACATGTGGGTGATGGTTTTGAGTTCATGAAACAGAATCAGGATGCCT
TTGATGTGATCATCACTGACTCCTCAGACCCTATGGGCCCCGCCGAAAGTCTCTTCAAAGAGTCCTATTACCAGCTCATG
AAGATGGCCCTCAAGGAAGATGGCATCCTCTGCTGCCAGGGTGAGTGCCAGTGGCTGCACCTGGACCTCATCAAGGAGAT
GTGGCAGTTCTGCCAGTCCCTGTTCCCCGTGGTGGCCTACGCCTACTGTACCATCCCCACCTACCCCGGTGGTCAGATCG
GCTTCATGCTGTGCAGCAAGAACCCGAGCACCAACTTCCAGGAGCCGGTGCAGCCGCTGACACAGCACCAGGTGGCGCAG
ATGCAGCTGAAGTACAACTCCGACGTGCACCGCGCCGCCTTCCTGCTGTCCGAGTTTGCCCGAAAGGCCCTGAATGATGT
GAGC

Alignment

ORF - retro_cjac_2131 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.26 %
• Parental protein coverage: 98.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GPAASGP-AAIREGWFRET-QLWPGQALSLQVEQLLHHRRSRYQDILVFRSKTYGNVLVLDGVIQCTERD
          GPAAS.P..AIR.GWFRET...WPGQALSLQV.QLLHHR.S.YQ.ILVF.SKTYGN.LVLDGVIQCTERD
Retrocopy GPAASAP<TAIRKGWFRETCSRWPGQALSLQVKQLLHHRHSCYQNILVFHSKTYGNMLVLDGVIQCTERD

Parental  EFSYQEMIANLPLCSHPNPQKVLIIGGGDGGVLREVVKHPSVESVVQCEIDEDVIQVSKKFLPGMAVGYS
          EFSYQEMIANLPLCSHPNPQKVLIIGGGD.GVL.EVVKHPSVESVV.CEIDEDVIQVSKKFLPGMAVGYS
Retrocopy EFSYQEMIANLPLCSHPNPQKVLIIGGGDRGVLCEVVKHPSVESVVHCEIDEDVIQVSKKFLPGMAVGYS

Parental  SSKLTLHVGDGFEFMKQNQDAFDVIITDSSDPMGPAESLFKESYYQLMKTALKEDGVLCCQGECQWLHLD
          SSKLTLHVGDGFEFMKQNQDAFDVIITDSSDPMGPAESLFKESYYQLMK.ALKEDG.LCCQGECQWLHLD
Retrocopy SSKLTLHVGDGFEFMKQNQDAFDVIITDSSDPMGPAESLFKESYYQLMKMALKEDGILCCQGECQWLHLD

Parental  LIKEMRQFCQSLFPVVAYAYCTIPTYPSGQIGFMLCSKNPSTNFQEPVQPLTQHQVAQMQLKYYNSDVHR
          LIKEM.QFCQSLFPVVAYAYCTIPTYP.GQIGFMLCSKNPSTNFQEPVQPLTQHQVAQMQLK.YNSDVHR
Retrocopy LIKEMWQFCQSLFPVVAYAYCTIPTYPGGQIGFMLCSKNPSTNFQEPVQPLTQHQVAQMQLK-YNSDVHR

Parental  AAFVLPEFARKALNDVS
          AAF.L.EFARKALNDVS
Retrocopy AAFLLSEFARKALNDVS

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	0.20 RPM	4.06 RPM
SRP051959_heart	0.46 RPM	3.82 RPM
SRP051959_kidney	0.47 RPM	3.59 RPM
SRP051959_liver	0.26 RPM	6.28 RPM
SRP051959_lung	0.44 RPM	3.35 RPM
SRP051959_lymph_node	0.16 RPM	4.68 RPM
SRP051959_skeletal_muscle	0.33 RPM	15.22 RPM
SRP051959_spleen	0.42 RPM	4.47 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2131 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2131 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2131 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002354	4 retrocopies	retro_cjac_2131 , retro_cjac_2524, retro_cjac_3331, retro_cjac_4025,
Dasypus novemcinctus	ENSDNOG00000013348	1 retrocopy	retro_dnov_338,
Homo sapiens	ENSG00000116649	2 retrocopies	retro_hsap_1426, retro_hsap_2313,
Gorilla gorilla	ENSGGOG00000014385	1 retrocopy	retro_ggor_1756,
Loxodonta africana	ENSLAFG00000028297	2 retrocopies	retro_lafr_1175, retro_lafr_894,
Macropus eugenii	ENSMEUG00000007002	2 retrocopies	retro_meug_1330, retro_meug_887,
Macaca mulatta	ENSMMUG00000019321	2 retrocopies	retro_mmul_1500, retro_mmul_2259,
Mus musculus	ENSMUSG00000006442	1 retrocopy	retro_mmus_3271,
Nomascus leucogenys	ENSNLEG00000009532	3 retrocopies	retro_nleu_1842, retro_nleu_2082, retro_nleu_2778,
Ochotona princeps	ENSOPRG00000012079	1 retrocopy	retro_opri_1119,
Pongo abelii	ENSPPYG00000001892	3 retrocopies	retro_pabe_1181, retro_pabe_1828, retro_pabe_2044,
Pan troglodytes	ENSPTRG00000000138	3 retrocopies	retro_ptro_1403, retro_ptro_1688, retro_ptro_975,