RetrogeneDB ID: retro_cjac_1344

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:57222899..57224125(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POU2F1
• Ensembl ID: ENSCJAG00000017095
• Aliases: None
• Description: POU class 2 homeobox 1 [Source:HGNC Symbol;Acc:9212]

Sequence

>retro_cjac_1344
ATGAACAACCGTCAGAAACCAGTAAACCATCTGTGGAGAGTGGAGATGGCAACACAGGCACACAAACCAATGGTCTGGAC
TTTCAGAAGCAGCCTGTGCCTGTAGGAGGAGCAATCTCAACAGCCCAGGTGCAGGCTTTCCTCGGACATCTTCATCAGGT
CCAACTCGATGGAACAAGTTTACAGGCTGCTGCTCAGTCTTTAAATGTACAGTCTAAATCTAATGAAGAATCGGGGGATT
CACAGCAGCCAAGCCAGCCTTCCCAGCAGCCTTCAGTGCAGGCAGCCATTCCCCAAATCCAGCTTATGCTAGCTGGAGGA
CAGATAACTGGGCTTACTTTGATGCTCGCCCAGCAACAGTTACTACTGCAGCAGGCACAGGCACAGGCACAGGCGCTGGC
TGCTGCAATACAGCAGCACTCCACCAGCCAGCAGCATAGCGCTGCTGGGGCCATCTTCTCTGCCTCTGCTGCCACACTCA
TGAGGCGGATCCCTCTGTCTCAGCCCATACAGATCGCACAGGATCTTTAAGAACTGCAACAGCTTCAACGGCAGAATCTC
AACCTGCAACAGTTTGTGTTGGTGCATCCAACCACCAATTTGCAGCCAGCGTGGTTTATCATCTCACAGACGCCCCAGGG
CCAGCAGGGTCTCCTGCAAATGCAAAATCTTTTATCACAACTACCTCAGCAAAGCCAAGACAACCACCTACAGTCGCAGC
CAAGCATCACCTTCACCTCACAGCCAGCAACCACAACACGCACGATAGCAGCAACCCCAATTCAGACACTTCCCCAGAGC
CAGTCAACACCAAAGCGAATTGATACTCCCAGCTTGGAGGAGCCCAGTGACCTTTAGGAGCTTCGGCAGTTTGCCAAGAC
CTTAAAACAAAGACGAATCAAATTCGGATTCACTCAGGCTAATGTTGGGCTTGCTATCAGGATACTATATGGAAATGACG
TCAGCCAAACTATCATCTCTCGCTTTGAAGCCTTGAACCTCAGCTTTAAGAACATGTGCAAGTTGAAGCCGCTTTTAGAG
AAGTGGCTAAATGATGCAGAGAACCTCTCATCTGATTCATCCTTCTCCAGCCCAAATGCCCTGAGTTCTCCAGGAATTGA
GGGCTCGAGCCATAGGAGGAAGAAACACGCCAGCATACAGACCAACATCCATGTGACCTTAGAGAAGAGTTTCTTGGAGA
ATCAAAATCCTACCTTGGAAGAGATC

Alignment

ORF - retro_cjac_1344 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.34 %
• Parental protein coverage: 55.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNN-PSETSKPSMESGDGNTGTQTNGLDFQKQPVPVGGAISTAQAQAFLGHLHQVQLAGTSLQAAAQSLN
          MNN.PSETSKPS.ESGDGNTGTQTNGLDFQKQPVPVGGAISTAQ.QAFLGHLHQVQL.GTSLQAAAQSLN
Retrocopy MNN<PSETSKPSVESGDGNTGTQTNGLDFQKQPVPVGGAISTAQVQAFLGHLHQVQLDGTSLQAAAQSLN

Parental  LQSKSNEESGDSQQPSQPSQQPSVQAAIPQTQLMLAGGQITGLTLTPAQQQLLLQQAQAQAQLLAAAVQQ
          .QSKSNEESGDSQQPSQPSQQPSVQAAIPQ.QLMLAGGQITGLTL..AQQQLLLQ........LAAA.QQ
Retrocopy VQSKSNEESGDSQQPSQPSQQPSVQAAIPQIQLMLAGGQITGLTLMLAQQQLLLQXXXXXXXXLAAAIQQ

Parental  HSASQQHSAAGATISASAATPMTQIPLSQPIQIAQDLQQLQQLQQQNLNLQQFVLVHPTTNLQPAQFIIS
          HS.SQQHSAAGA..SASAAT.M..IPLSQPIQIAQDL..LQQLQ.QNLNLQQFVLVHPTTNLQPA.FIIS
Retrocopy HSTSQQHSAAGAIFSASAATLMRRIPLSQPIQIAQDL*ELQQLQRQNLNLQQFVLVHPTTNLQPAWFIIS

Parental  QTPQGQQGLLQAQNLLTQLPQQSQANLLQSQPSITLTSQPATPTRTIAATPIQTLPQSQSTPKRIDTPSL
          QTPQGQQGLLQ.QNLL.QLPQQSQ.N.LQSQPSIT.TSQPAT.TRTIAATPIQTLPQSQSTPKRIDTPSL
Retrocopy QTPQGQQGLLQMQNLLSQLPQQSQDNHLQSQPSITFTSQPATTTRTIAATPIQTLPQSQSTPKRIDTPSL

Parental  EEPSDLEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLEKW
          EEPSDL.EL.QFAKT.KQRRIK.GFTQ..VGLA...LYGND.SQT.ISRFEALNLSFKNMCKLKPLLEKW
Retrocopy EEPSDL*ELRQFAKTLKQRRIKFGFTQANVGLAIRILYGNDVSQTIISRFEALNLSFKNMCKLKPLLEKW

Parental  LNDAENLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEI
          LNDAENLSSDSS.SSP.AL.SPGIEG.S.RRKK..SI.TNI.V.LEKSFLENQ.PT.EEI
Retrocopy LNDAENLSSDSSFSSPNALSSPGIEGSSHRRKKHASIQTNIHVTLEKSFLENQNPTLEEI

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	0.18 RPM	6.39 RPM
SRP051959_heart	0.11 RPM	6.07 RPM
SRP051959_kidney	0.13 RPM	7.17 RPM
SRP051959_liver	0.06 RPM	2.51 RPM
SRP051959_lung	0.11 RPM	7.92 RPM
SRP051959_lymph_node	0.16 RPM	11.44 RPM
SRP051959_skeletal_muscle	0.15 RPM	6.49 RPM
SRP051959_spleen	0.13 RPM	10.19 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1344 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1344 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1344 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017095	1 retrocopy	retro_cjac_1344 ,
Callithrix jacchus	ENSCJAG00000019789	1 retrocopy	retro_cjac_123,
Myotis lucifugus	ENSMLUG00000015231	1 retrocopy	retro_mluc_780,