RetrogeneDB ID: retro_cjac_950

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:130218095..130218941(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023299
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000008021
• Aliases: None
• Description: Purine nucleoside phosphorylase A [Source:UniProtKB/TrEMBL;Acc:F7I6R4]

Sequence

>retro_cjac_950
ATGGCTTCAAGCACCACCACCACTGTCGTGAAGATTGGAATAATTGGTGGAACAGGCCTGGATGATCCAGAAATTTTAGA
AGGAAGAACTGAAAAATATGTGGATACTCCATTTGGCAAGCCATCTGATGCCTTAATTTTGGGGAAGATAAACGTTGATT
GCGTCCTCCTTGCAAGGCATGGGAGGCAGCACACCATCATGCCTTCAAAAGTCAACTACCAGGCAAACATCTGGGCTTTG
AAGGAAGAGGGATGTACACATGTCATAGTGACCACAGCTTGTGGCTCTTTGAGGGAGGAGATTCAGCCCGGCGATATTGT
CATTATTGATCAGTTCATTGACAGGACCACTATGAGACCACAGTCCTTCTATGATGGAAGTCATTCTTGTGCCAGAGGAG
TGTGCCATATTCCAATGGCCGAGCCGTTTTGCCCCAAAACGAGAGAGGTTCTTATAGAGACTGCTAAGAAGCTAGGACTC
CGGTGCCACTCAAAGGGGACAATGGCCACAATTGAGGGACCTCGTTTTAGCTCCCGGGCAGAAAGCTTCATGCTCCGCAC
CTGGGGGGCAGATGTTATCAACATGACTACAGTTCCGGAGGTGGTTCTTGCTAAGGAGGCTGGAATTTGTTATGCAAGTA
TCGCCATGGCGACAGATTATGACTGCTGGAAGGAGCATGAGGAAGCAGTTTTGGTGGACCGGGTCTTAAAGACTCTGAAA
GAAAATGCTAATAAAACCAAAAGTTTACTGCTCACTACCATACCTCAGATAGGGTCCATGGAATGGTCAGAAACCCTCCA
TAGCCTGAAGAATATGGCCCAGTTTTCTGTTTTATTACCAAGACAT

Alignment

ORF - retro_cjac_950 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.59 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASSTTTTVVKIGIIGGTGLDDPEILEGRTEKYVDTPFGKPSDALILGKIKNVDCVLLARHGRQHTIMPS
          MASSTTTTVVKIGIIGGTGLDDPEILEGRTEKYVDTPFGKPSDALILGKI.NVDCVLLARHGRQHTIMPS
Retrocopy MASSTTTTVVKIGIIGGTGLDDPEILEGRTEKYVDTPFGKPSDALILGKI-NVDCVLLARHGRQHTIMPS

Parental  KVNYQANIWALKEEGCTHVIVTTACGSLREEIQPGDIVIIDQFIDRTTMRPQSFYDGSHSCARGVCHIPM
          KVNYQANIWALKEEGCTHVIVTTACGSLREEIQPGDIVIIDQFIDRTTMRPQSFYDGSHSCARGVCHIPM
Retrocopy KVNYQANIWALKEEGCTHVIVTTACGSLREEIQPGDIVIIDQFIDRTTMRPQSFYDGSHSCARGVCHIPM

Parental  AEPFCPKTREVLIETAKKLGLRCHSKGTMVTIEGPRFSSRAESFMLRTWGADVINMTTVPEVVLAKEAGI
          AEPFCPKTREVLIETAKKLGLRCHSKGTM.TIEGPRFSSRAESFMLRTWGADVINMTTVPEVVLAKEAGI
Retrocopy AEPFCPKTREVLIETAKKLGLRCHSKGTMATIEGPRFSSRAESFMLRTWGADVINMTTVPEVVLAKEAGI

Parental  CYASIAMATDYDCWKEHEEAVSVDRVLKTLKENANKAKSLLLTTIPQIGSMEWSETLHSLKNMAQFSVLL
          CYASIAMATDYDCWKEHEEAV.VDRVLKTLKENANK.KSLLLTTIPQIGSMEWSETLHSLKNMAQFSVLL
Retrocopy CYASIAMATDYDCWKEHEEAVLVDRVLKTLKENANKTKSLLLTTIPQIGSMEWSETLHSLKNMAQFSVLL

Parental  PRH
          PRH
Retrocopy PRH

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	0.07 RPM	6.37 RPM
SRP051959_heart	0.18 RPM	4.88 RPM
SRP051959_kidney	0.22 RPM	7.50 RPM
SRP051959_liver	0.69 RPM	8.25 RPM
SRP051959_lung	0.05 RPM	5.95 RPM
SRP051959_lymph_node	0.14 RPM	7.76 RPM
SRP051959_skeletal_muscle	0.04 RPM	3.49 RPM
SRP051959_spleen	0.23 RPM	9.50 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_950 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_950 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_950 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000025929	1 retrocopy	retro_btau_1049,
Choloepus hoffmanni	ENSCHOG00000002224	1 retrocopy	retro_chof_772,
Callithrix jacchus	ENSCJAG00000008021	2 retrocopies	retro_cjac_187, retro_cjac_950 ,
Cavia porcellus	ENSCPOG00000000825	1 retrocopy	retro_cpor_375,
Dasypus novemcinctus	ENSDNOG00000008670	1 retrocopy	retro_dnov_1572,
Echinops telfairi	ENSETEG00000013214	1 retrocopy	retro_etel_588,
Macropus eugenii	ENSMEUG00000015381	2 retrocopies	retro_meug_807, retro_meug_917,
Microcebus murinus	ENSMICG00000015072	1 retrocopy	retro_mmur_927,
Macaca mulatta	ENSMMUG00000001137	1 retrocopy	retro_mmul_1549,
Ornithorhynchus anatinus	ENSOANG00000013963	1 retrocopy	retro_oana_38,
Oryctolagus cuniculus	ENSOCUG00000012289	2 retrocopies	retro_ocun_1355, retro_ocun_341,
Otolemur garnettii	ENSOGAG00000007889	1 retrocopy	retro_ogar_3285,
Ochotona princeps	ENSOPRG00000001259	1 retrocopy	retro_opri_792,