RetrogeneDB ID: retro_cjac_2284

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:139536049..139536907(-)
• Located in intron of: ENSCJAG00000018458

Retrocopy information

• Ensembl ID: ENSCJAG00000018465
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000015267
• Aliases: None
• Description: None

Sequence

>retro_cjac_2284
TTGGCTAATGACGCCGCTGCAGGGGGGTGGGTGGGGGGCGGAGGCCCTGGGGGCCCTGGGATGGGGAACTGCAGTGGCTT
CCGCGGAGGTTTCAGCAGTGGCATCCGGGCCGGGGTCACCACCGTGGATGGGCCGGGACGAGGCTGTGGAGCTCATGGAG
GCAAGGCCGAGGATAAGGATTGGATGCCTGTCACTAAGTTAGGCCGCTTGGTCAAGGACATGAAGATCAAGTCTCTGGAG
GAGACCTATCTCTTCCCTCTGCCCATCAAGGAATCTGAGATCACTGAATTTTTCCTAGGGGCCTCTCTTAAGGATGAGGT
TTTGAAGATTATGCCGGTACAGAAGCAGACCTGTGCTGGCCAGCCCACCAGGTTCAAGGCGTTTGTTGCTATTGGGGACT
ACAATGGCCATGTTGGACTGGGTGTTAAGTGTTCCAAGGAGGTGGACACTGCCATCCGTGGGGCCATCATCTTGGCCAAG
CTCTCCACTGTGCCGTGCGCTGAGGCTACTGGGGAACAAGATCGGCAAGCCCCACACCGTCCCTTGCAAAGTGACAGGCC
TCTGTGGCTCTGTGCTGGTATGCCTCATCCCCACACCCAGGGGCACTAGCATCGTCTCAGTACCTGTGCCCAAGAAGCTG
CTCATGATGGCTGGTATCAATGACTGCCACACCTCAGCCAGGGGCTGCACTGCCACCCTGGGCAACTTCGCCAAGGTCAC
CTTTGATGCTATCTCTAAGACTTACAGCTACCTGACACCCAGTCTCTGGAAGGAGACTGTATTACCAAGTCTCCCTATCA
GGAATTCATTGACCACCTCGTCAAGACCCACACCAGAATCTCCATGCAGAGGACTCAG

Alignment

ORF - retro_cjac_2284 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.85 %
• Parental protein coverage: 97.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MADDAGAAG--APGGPGGPGMGNRGGFRGGFGSGIRGRGRGRGRGRGRGRGARGGKAEDKEWMPVTKLGR
          .A.DA.A.G....GGPGGPGMGN..GFRGGF.SGIR..G.....G.GRG.GA.GGKAEDK.WMPVTKLGR
Retrocopy LANDAAAGGWVGGGGPGGPGMGNCSGFRGGFSSGIRA-GVTTVDGPGRGCGAHGGKAEDKDWMPVTKLGR

Parental  LVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVG
          LVKDMKIKSLEE.YLF.LPIKESEI..FFLGASLKDEVLKIMPVQKQT.AGQ.TRFKAFVAIGDYNGHVG
Retrocopy LVKDMKIKSLEETYLFPLPIKESEITEFFLGASLKDEVLKIMPVQKQTCAGQPTRFKAFVAIGDYNGHVG

Parental  LGVKCSKEVATAIRGAIILAKLSIVP-VRRGYW-GNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVS
          LGVKCSKEV.TAIRGAIILAKLS.VP.VR.GYW.GNKIGKPHTVPCKVTG.CGSVLV.LIP.PRGT.IVS
Retrocopy LGVKCSKEVDTAIRGAIILAKLSTVP<VR*GYW<GNKIGKPHTVPCKVTGLCGSVLVCLIPTPRGTSIVS

Parental  APVPKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKETV-FTKSPYQEFTDHLVK
          .PVPKKLLMMAGI.DC.TSARGCTATLGNFAK.TFDAISKTYSYLTP.LWKETV..TKSPYQEF.DHLVK
Retrocopy VPVPKKLLMMAGINDCHTSARGCTATLGNFAKVTFDAISKTYSYLTPSLWKETV<ITKSPYQEFIDHLVK

Parental  THTRVSVQRTQ
          THTR.S.QRTQ
Retrocopy THTRISMQRTQ

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	0.69 RPM	103.33 RPM
SRP051959_heart	0.28 RPM	66.13 RPM
SRP051959_kidney	0.38 RPM	86.90 RPM
SRP051959_liver	0.32 RPM	169.21 RPM
SRP051959_lung	0.75 RPM	76.34 RPM
SRP051959_lymph_node	0.62 RPM	130.47 RPM
SRP051959_skeletal_muscle	0.24 RPM	155.73 RPM
SRP051959_spleen	0.38 RPM	120.76 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2284 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2284 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2284 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 88 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002549	1 retrocopy	retro_acar_57,
Callithrix jacchus	ENSCJAG00000015267	15 retrocopies	retro_cjac_1482, retro_cjac_1585, retro_cjac_1609, retro_cjac_1712, retro_cjac_1964, retro_cjac_2201, retro_cjac_2255, retro_cjac_2284 , retro_cjac_2361, retro_cjac_2493, retro_cjac_2620, retro_cjac_274, retro_cjac_317, retro_cjac_3741, retro_cjac_4194,
Felis catus	ENSFCAG00000029191	6 retrocopies	retro_fcat_1245, retro_fcat_1328, retro_fcat_1606, retro_fcat_1610, retro_fcat_1737, retro_fcat_517,
Macropus eugenii	ENSMEUG00000004508	2 retrocopies	retro_meug_156, retro_meug_2103,
Microcebus murinus	ENSMICG00000012765	28 retrocopies	retro_mmur_1192, retro_mmur_1273, retro_mmur_1283, retro_mmur_1296, retro_mmur_1407, retro_mmur_1417, retro_mmur_1440, retro_mmur_153, retro_mmur_1613, retro_mmur_205, retro_mmur_210, retro_mmur_226, retro_mmur_230, retro_mmur_259, retro_mmur_266, retro_mmur_463, retro_mmur_672, retro_mmur_698, retro_mmur_742, retro_mmur_802, retro_mmur_824, retro_mmur_829, retro_mmur_875, retro_mmur_953, retro_mmur_966, retro_mmur_969, retro_mmur_981, retro_mmur_99,
Monodelphis domestica	ENSMODG00000016077	1 retrocopy	retro_mdom_536,
Sarcophilus harrisii	ENSSHAG00000015213	5 retrocopies	retro_shar_186, retro_shar_288, retro_shar_456, retro_shar_525, retro_shar_783,
Tupaia belangeri	ENSTBEG00000006726	30 retrocopies	retro_tbel_1023, retro_tbel_1059, retro_tbel_1105, retro_tbel_1179, retro_tbel_129, retro_tbel_1444, retro_tbel_1545, retro_tbel_1615, retro_tbel_1622, retro_tbel_1786, retro_tbel_1910, retro_tbel_2294, retro_tbel_2749, retro_tbel_2786, retro_tbel_2973, retro_tbel_3179, retro_tbel_3314, retro_tbel_3509, retro_tbel_3523, retro_tbel_3682, retro_tbel_3701, retro_tbel_392, retro_tbel_4373, retro_tbel_463, retro_tbel_4674, retro_tbel_481, retro_tbel_586, retro_tbel_603, retro_tbel_639, retro_tbel_647,