RetrogeneDB ID: retro_cjac_1622

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:3050800..3051423(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000004474
• Aliases: None
• Description: None

Sequence

>retro_cjac_1622
AATCCAGCCAGCTTCACCATTACTGTGACATCTGAGGCTGGAGGAAATGATGAAACTGTCCAGACTACCCTTAAGTTGAC
AGACAGGGAGAAATACCCAGATAAAGCTTGTCTTTATGAAGTATTCTCAGAAAATCTAGAAGATAATGTCTCAGACATTT
AAAAATTCTTAGCATTACAAACCAAAGAAAATATTGGTATGGTGATAATCTTTAGTGACAGCCATGCAAGAAAAATTAAA
TGAAATAGATCAGATAAAATCTAGAAGAGAAGAAAAAAAGAAACAAAAAAAAAATCAAAATAAACTGGAAGGCAATTATT
TCATAATATTCCTGTTATTATTGAGAAGTTCTTAAACTGGAAGGCCAAGTTTAATGCAGAAGTCTTGGAAATTAAAAAGA
AATGGATAGAAAAAGATCAAGCAGGAAAAAATAAATTAAGTGGGAAACAGCTACTTGAAACAGATCCAAATCTCGACACA
TTTGATATCCAGTTCTCGGAGGATGCTGGAAACAATGTGGAGTTAATTGAGTCTTTGTTCCAGGAAATGGATGACCTGGG
GCTGGGGGATGAGGAGGTGATTCAGACTCCAATCCTGCTGACCCAGAAAGTGACTCCACTGAC

Alignment

ORF - retro_cjac_1622 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.05 %
• Parental protein coverage: 88.43 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SPPSFTITVTSEAGEYDETVQTTLKFTYSEKYPDEAPLYEIFSQENLEDNDISDILKLLALQAEENLGMV
          .P.SFTITVTSEAG..DETVQTTLK.T..EKYPD.A.LYE.FS.ENLEDN..SDI.K.LALQ..EN.GMV
Retrocopy NPASFTITVTSEAGGNDETVQTTLKLTDREKYPDKACLYEVFS-ENLEDN-VSDI*KFLALQTKENIGMV

Parental  MIFTLVTAVQEKLNEIVDQIKLEERRKETKRKEAEEAEKQLFHGTPVTIENFLNWKAKFDAELLEIKKKR
          .IF....A...K.N...D.I........TK.K.......QLFH..PV.IE.FLNWKAKF.AE.LEIKKK.
Retrocopy IIFSDSHARKIK*NR-SDKI*KRRKKE-TKKK-SK*TGRQLFHNIPVIIEKFLNWKAKFNAEVLEIKKKW

Parental  MKEEEQAGKNKLSGKQLFETDHNLDTSDIQFLEDAGNNVEVDESLFQEMDDLELEDDE-DDPDYTPADPE
          ..E..QAGKNKLSGKQL.ETD.NLDT.DIQF.EDAGNNVE..ESLFQEMDDL.L.D.E..D.D..PADPE
Retrocopy I-EKDQAGKNKLSGKQLLETDPNLDTFDIQFSEDAGNNVELIESLFQEMDDLGLGDEE<GDSDSNPADPE

Parental  SDSAD
          SDS.D
Retrocopy SDSTD

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	10.38 RPM
SRP051959_heart	0.00 RPM	12.65 RPM
SRP051959_kidney	0.00 RPM	12.38 RPM
SRP051959_liver	0.00 RPM	9.10 RPM
SRP051959_lung	0.00 RPM	10.79 RPM
SRP051959_lymph_node	0.00 RPM	11.46 RPM
SRP051959_skeletal_muscle	0.11 RPM	15.94 RPM
SRP051959_spleen	0.00 RPM	13.21 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1622 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1622 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1622 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005692	1 retrocopy	retro_amel_991,
Bos taurus	ENSBTAG00000009689	1 retrocopy	retro_btau_1004,
Callithrix jacchus	ENSCJAG00000004474	1 retrocopy	retro_cjac_1622 ,
Dasypus novemcinctus	ENSDNOG00000007516	1 retrocopy	retro_dnov_2467,
Equus caballus	ENSECAG00000006587	2 retrocopies	retro_ecab_216, retro_ecab_277,
Echinops telfairi	ENSETEG00000019085	3 retrocopies	retro_etel_140, retro_etel_1992, retro_etel_423,
Loxodonta africana	ENSLAFG00000008170	1 retrocopy	retro_lafr_813,
Monodelphis domestica	ENSMODG00000017837	1 retrocopy	retro_mdom_1686,
Oryctolagus cuniculus	ENSOCUG00000013592	1 retrocopy	retro_ocun_691,
Procavia capensis	ENSPCAG00000005016	1 retrocopy	retro_pcap_114,
Ictidomys tridecemlineatus	ENSSTOG00000020231	2 retrocopies	retro_itri_121, retro_itri_365,
Tupaia belangeri	ENSTBEG00000002543	2 retrocopies	retro_tbel_2986, retro_tbel_4366,