RetrogeneDB ID: retro_cjac_1279

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:50162911..50163342(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000032248
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000038151
• Aliases: None
• Description: None

Sequence

>retro_cjac_1279
TCATGGATTCAGGAGTTCAAAGAGGCCTTCAACATGACTGATCAGAACAGAGATGCTTTCATTGACAAGGAAGATTTGCG
TGATATACTTGCTTCATTTGGGAAGAATCTAACTGATGAGTATTTGGATGTCACGATGAATGAGGCTCCAGGCCTCATCA
ATTTCACCATGTTCCTCACCATGTTTGGTGAGAAGTTAAATGCCACAGATCGTGACGATGTCATCAGAAATGCTTTTGCT
TGCTTTGATAAAGAAGCAACTGGCACCATTCAGGAAGATTACCTGAGAGAGTTGCTGACACCATAGGGGAAAAGTTTATG
GATGAGGAAGTGGATGAGCTGTACAGAGAAGCACCTATTGACAAAAAGTGGAACTTCAATTACATCGAGTTCACACACAT
CTGGAAACATGGAGCAAATGATCAAGATGAC

Alignment

ORF - retro_cjac_1279 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.45 %
• Parental protein coverage: 83.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SQIQEFKEAFNMIDQNRDGFIDKEDLHDMLASLGKNPTDEYLDAMMNEAPGPINFTMFLTMFGEKLNGTD
          S.IQEFKEAFNM.DQNRD.FIDKEDL.D.LAS.GKN.TDEYLD..MNEAPG.INFTMFLTMFGEKLN.TD
Retrocopy SWIQEFKEAFNMTDQNRDAFIDKEDLRDILASFGKNLTDEYLDVTMNEAPGLINFTMFLTMFGEKLNATD

Parental  PEDVIRNAFACFDEEATGTIQEDYLRELLT-TMGDRFTDEEVDELYREAPIDKKGNFNYIEFTRILKHGA
          ..DVIRNAFACFD.EATGTIQEDYLRELLT.T.G..F.DEEVDELYREAPIDKK.NFNYIEFT.I.KHGA
Retrocopy RDDVIRNAFACFDKEATGTIQEDYLRELLT<TIGEKFMDEEVDELYREAPIDKKWNFNYIEFTHIWKHGA

Parental  KDKDD
          .D.DD
Retrocopy NDQDD

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	39.65 RPM
SRP051959_heart	0.00 RPM	103.33 RPM
SRP051959_kidney	0.00 RPM	34.83 RPM
SRP051959_liver	0.00 RPM	24.82 RPM
SRP051959_lung	0.02 RPM	71.27 RPM
SRP051959_lymph_node	0.00 RPM	56.50 RPM
SRP051959_skeletal_muscle	0.00 RPM	249.24 RPM
SRP051959_spleen	0.00 RPM	57.86 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1279 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1279 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1279 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 81 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016024	2 retrocopies	retro_btau_1273, retro_btau_1693,
Canis familiaris	ENSCAFG00000029134	3 retrocopies	retro_cfam_166, retro_cfam_583, retro_cfam_79,
Choloepus hoffmanni	ENSCHOG00000005206	54 retrocopies	retro_chof_1002, retro_chof_1149, retro_chof_1238, retro_chof_1250, retro_chof_1273, retro_chof_1321, retro_chof_1326, retro_chof_135, retro_chof_1352, retro_chof_1363, retro_chof_1374, retro_chof_1439, retro_chof_1505, retro_chof_1520, retro_chof_1538, retro_chof_1553, retro_chof_1574, retro_chof_1594, retro_chof_1608, retro_chof_1641, retro_chof_1694, retro_chof_1783, retro_chof_1790, retro_chof_1798, retro_chof_1801, retro_chof_1804, retro_chof_1809, retro_chof_1875, retro_chof_1879, retro_chof_1887, retro_chof_2059, retro_chof_2114, retro_chof_2157, retro_chof_2180, retro_chof_2353, retro_chof_2430, retro_chof_2492, retro_chof_2510, retro_chof_2516, retro_chof_2597, retro_chof_2638, retro_chof_2639, retro_chof_2689, retro_chof_543, retro_chof_545, retro_chof_584, retro_chof_606, retro_chof_618, retro_chof_667, retro_chof_686, retro_chof_696, retro_chof_729, retro_chof_752, retro_chof_949,
Callithrix jacchus	ENSCJAG00000012890	4 retrocopies	retro_cjac_3193, retro_cjac_3195, retro_cjac_3743, retro_cjac_637,
Callithrix jacchus	ENSCJAG00000038151	2 retrocopies	retro_cjac_1279 , retro_cjac_3119,
Echinops telfairi	ENSETEG00000011271	3 retrocopies	retro_etel_393, retro_etel_439, retro_etel_96,
Microcebus murinus	ENSMICG00000017884	2 retrocopies	retro_mmur_1194, retro_mmur_1585,
Mus musculus	ENSMUSG00000024048	1 retrocopy	retro_mmus_1149,
Otolemur garnettii	ENSOGAG00000001340	7 retrocopies	retro_ogar_1877, retro_ogar_2516, retro_ogar_2536, retro_ogar_2540, retro_ogar_347, retro_ogar_517, retro_ogar_605,
Sorex araneus	ENSSARG00000011512	1 retrocopy	retro_sara_102,
Ictidomys tridecemlineatus	ENSSTOG00000027658	2 retrocopies	retro_itri_1480, retro_itri_896,