RetrogeneDB ID: retro_cjac_1280

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:52256180..52258606(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRRM1
• Ensembl ID: ENSCJAG00000020822
• Aliases: None
• Description: serine/arginine repetitive matrix 1 [Source:HGNC Symbol;Acc:16638]

Sequence

>retro_cjac_1280
ATGGACGCAGGATTCTTCCGCGGAACATGTGCAGAACAGGATAATCGGTTCAGCAACAAACAGAAGAAACTACTGAAGCA
GCTGAAATTTGCAGAATGCCTAGAAAAAAAGGTGGGCACGAGCAAAGTAAATTTGGAAGTTATAAAGCCTTGGATAACAA
AAAGAGTAACAGAAATCCGTGGGTTTAAAGATGATGTTGTGATTGAGTTTATATTCAACCAGCTGGAAGTGAAGAATCCA
GACTCCAAAATGATACAAATCAACCTGACTGGATTTTTAAACGGAAAAAATGCGCGAGAATTTATGGGAGAACTGTGGCC
CCTGCTGCTAAGTGCACAAGAAAACGTCGCGGGAATCCCTTCTGCTTTCCTAGAGCTGAAGAAAGAAGAAATAAAACAAA
GACAGATTGAACAAGAAAAATGGGCATTTATGAAAAAGCAAGATGAAGACAAAGATAAAAGGGATAAGGAAGAGAAAGAA
AGCAGCAGAGAAAAAAGGGAGAGGTCTGGTAGCCCAAGAAGATGCAAATCCAGATCTCCTTCCCCTAGAAGACGACCTTC
CCCTGTCAGGAGAGAGAGAAAGCGCAGTCATTCTCGATCTCCCGGTCACAGAACCAAGAGCCGGAGTCCTTCCCCTGCTC
CAGAAAAGAAGGAAAAAACTCCAGAGCTCCCAGAACCTTCAGTGAAAGTAAAAGAACCTTCAGTACAAGAGGCCACTTCT
ACTAGTGACATTCTGAAAGTTCCCAAACCTGAACCTGTACCAGAGCCTAAAGAACCTTCTCCAGAAAAAAATTCCAAAAA
AGAAAAGGAGAAGGAAAAGACCCGACCACGATCTCGGTCATGCTCCAAATCAAGATCCTGGACGCGGTCCCGCTCTCCTT
CTCACACTCGACCTAGATGGCACCATAGATCTCGATCGAGATCATATTCACCTAGAAGGTGGCCAAGCCCAAGAAGGCGG
CCATCTCCTCGAAGAAGAACTCCACTAAGGAGAATGCCTCCTCCACCAAGGCATAGAAGCAGCAGATCACCAGTAAGACG
AAGAAGACGTTCGTCAGCATCCTTGTCTGGGAGTAGCTCATCATCCTCTTCATCTCGTTCCCGGTCACCACCAAAGAAAC
CGCCCAAGAGGACATCCAGCCCCCCTCGAAAAACTCGTAGGTTATCTCCTTCAGCAAGTCCTCTAAGGCGAAGGCACAGG
CCATCACCTCCTGCAACTCCACCACCCCAAACTCGGCATTCCCCAACACCCCAGCAGTCAAACTGTACAAGAAAAAGTCG
TGTTTCCATGTCTCCAGGGAGAACTTCAGTAACAAAACATAAAGGTACTGAGAAAAGAGAATCCCCTTCACCAGCACCGA
AGCCTAGAAAAGTAGAGTTATCTAAATCGGAAGAAGATAAAGGTGGCAAAATGGCTGCAGCAGATTCTGTGCAGCAGAGA
CGTCAATACCGACGATAAAAGCAGCAGTCTTTGTCTGACTCTGGCTCCTCCTCCTCACAAGATGAAAGACCCAAGAGATC
CCATGTGAAGAATGGTGAGGTTGGCAGGCGGCGGAGACATTCCCCTTCCCAGAGTGCCTCTCCATCACCACGACAGCGCC
AAAAAGAGACATCCCCTCGGATGCAGATGGGAAAGCGATGGCAATCGCCAGTGACTAAAAGTGGTAGACGGAGGAGAAGT
CCAACCCCACCACCCACCAGAAGGCGACGGTCTCCTTCGCCCACCCCTCCTCCTCGACAGCGCAGGTCTCCCACACCACC
ACCACGACGAAGGACTCCTTCTCCACCCCCACGTCGGCGCTCACCTTCTCCTAGAAGATATTCTCCTCCAATACAGAGGA
GATACTCTCCTTCTCCTCCTCCCCCTCCTAAACGAAGGGCATCACCATCTCCATCACCAAAGCATCGGGTCTCCCATTCT
CCACCTCCCAAACAAAGAAGCTCCCCAGTCACCAAGAGACGTTCACCTTCATTATCATCCAAGCATAGGAAAGGGTCTTC
CCCAAGCCGGTCTATGCGGGAGGCCCGATCACCACAACCAAACAAACGGCATTTGCCCTCACCACGGCCTCCAGCTCCTC
AGACCTCCTCAAGTCCTCCACCTGTTCGAAGAGGAGCGTCCTCATCACCCCAAAGAAGACAGTCCCCATCTCCAAGTACT
AGGCCCATTAGGAGAGTCGCCAGGACTCCGGAACCTAAAAAGATAAAAAAGGCTGCTTCACCAAGCCCACAGTCTGTAAC
AGGGTCTCATCCTCCCGATCTGTCTCTGGGTCTCCTGAGCCAACAGTTAAAAAGCCCCCAGCACCTCCGTCCCCCATCCA
GTCTCAGTCACCGCCTACAAACTGGTCACCAGCTGTACGGATCAAAAAGGCCAAAAGCCCGACACCAAGCCCATCACCGC
CAAGAAATTTGGATCAAGAAGGAGGT

Alignment

ORF - retro_cjac_1280 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.06 %
• Parental protein coverage: 89.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDAGFFRGTSAEQDNRFSNKQKKLLKQLKFAECLEKKVDMSKVNLEVIKPWITKRVTEILGFEDDVVIEF
          MDAGFFRGT.AEQDNRFSNKQKKLLKQLKFAECLEKKV..SKVNLEVIKPWITKRVTEI.GF.DDVVIEF
Retrocopy MDAGFFRGTCAEQDNRFSNKQKKLLKQLKFAECLEKKVGTSKVNLEVIKPWITKRVTEIRGFKDDVVIEF

Parental  IFNQLEVKNPDSKMMQINLTGFLNGKNAREFMGELWPLLLSAQENIAGIPSAFLELKKEEIKQRQIEQEK
          IFNQLEVKNPDSKM.QINLTGFLNGKNAREFMGELWPLLLSAQEN.AGIPSAFLELKKEEIKQRQIEQEK
Retrocopy IFNQLEVKNPDSKMIQINLTGFLNGKNAREFMGELWPLLLSAQENVAGIPSAFLELKKEEIKQRQIEQEK

Parental  LASMKKQDEDKDKRDKEEKESSREKRERSRSPRRRKSRSPSPRRRSSPVRRERKRSHSRSPRHRTKSRSP
          .A.MKKQDEDKDKRDKEEKESSREKRERS.SPRR.KSRSPSPRRR.SPVRRERKRSHSRSP.HRTKSRSP
Retrocopy WAFMKKQDEDKDKRDKEEKESSREKRERSGSPRRCKSRSPSPRRRPSPVRRERKRSHSRSPGHRTKSRSP

Parental  SPAPEKKEKTPELPEPSVKVKEPSVQEATSTSDILKVPKPEPVPEPKEPSPEKNSKKEKEKEKTRPRSRS
          SPAPEKKEKTPELPEPSVKVKEPSVQEATSTSDILKVPKPEPVPEPKEPSPEKNSKKEKEKEKTRPRSRS
Retrocopy SPAPEKKEKTPELPEPSVKVKEPSVQEATSTSDILKVPKPEPVPEPKEPSPEKNSKKEKEKEKTRPRSRS

Parental  RSKSRSRTRSRSPSHTRPRRRHRSRSRSYSPRRRPSPRRRPSPRRRTPPRRMPPPPRHRRSRSPVRRRRR
          .SKSRS.TRSRSPSHTRPR..HRSRSRSYSPRR.PSPRRRPSPRRRTP.RRMPPPPRHR.SRSPVRRRRR
Retrocopy CSKSRSWTRSRSPSHTRPRWHHRSRSRSYSPRRWPSPRRRPSPRRRTPLRRMPPPPRHRSSRSPVRRRRR

Parental  SSASLSGSSSSSSSSRSRSPPKKPPKRTSSPPRKTRRLSPSASPPRRRHRPSPPATPPPKTRHSPTPQQS
          SSASLSGSSSSSSSSRSRSPPKKPPKRTSSPPRKTRRLSPSASP.RRRHRPSPPATPPP.TRHSPTPQQS
Retrocopy SSASLSGSSSSSSSSRSRSPPKKPPKRTSSPPRKTRRLSPSASPLRRRHRPSPPATPPPQTRHSPTPQQS

Parental  NRTRKSRVSVSPGRTSGKVTKHKGTEKRESPSPAPKPRKVELSESEEDKGGKMAAADSVQQRRQYRRQNQ
          N.TRKSRVS.SPGRTS..VTKHKGTEKRESPSPAPKPRKVELS.SEEDKGGKMAAADSVQQRRQYRR..Q
Retrocopy NCTRKSRVSMSPGRTS--VTKHKGTEKRESPSPAPKPRKVELSKSEEDKGGKMAAADSVQQRRQYRR*KQ

Parental  QSSSDSGSSSSSEDERPKRSHVKNGEVGRRRRHSPSRSASPSPRKRQKETSPR---GRRRRSPTPPPTRR
          QS.SDSG.SSSS.DERPKRSHVKNGEVGRRRRHSPS.SASPSPR.RQKETSPR...G.R..SP.....RR
Retrocopy QSLSDSG-SSSSQDERPKRSHVKNGEVGRRRRHSPSQSASPSPRQRQKETSPRMQMGKRWQSPVTKSGRR

Parental  RRSPSPAPPPRRRR--SPTPPPR-RRTPSPPPRRRSPS-PRRYSPPIQRRYSPSPPPKRRTASPPPPPKR
          RRSP.P.PP.RRRR..SPTPPPR.RR.P.PPPRRR.PS.P.R...P..RRYSP.P...R...SPPPPPKR
Retrocopy RRSPTP-PPTRRRRSPSPTPPPRQRRSPTPPPRRRTPSPPPRRRSPSPRRYSP-PIQRRYSPSPPPPPKR

Parental  RASPSPPPKHRVSHSPPPKQRSSPVTKRRSPSLSSKHRKGSSPSRSTREARSPQPNKRHSPSPRPRAPQT
          RASPSP.PKHRVSHSPPPKQRSSPVTKRRSPSLSSKHRKGSSPSRS.REARSPQPNKRH.PSPRP.APQT
Retrocopy RASPSPSPKHRVSHSPPPKQRSSPVTKRRSPSLSSKHRKGSSPSRSMREARSPQPNKRHLPSPRPPAPQT

Parental  SSSPPPVRRGTSSSPQRRQSPSPSTRPIRRVSRTPEPKKIKKAASPSPQSI-RRVSSSRSVSGSPEPAVK
          SSSPPPVRRG.SSSPQRRQSPSPSTRPIRRV.RTPEPKKIKKAASPSPQS...RVSSSRSVSGSPEP.VK
Retrocopy SSSPPPVRRGASSSPQRRQSPSPSTRPIRRVARTPEPKKIKKAASPSPQSV<NRVSSSRSVSGSPEPTVK

Parental  KPPAPPSPIQSQSPSTNWSPAVPIKKAKSPTPSPSPPRNSDQEGG
          KPPAPPSPIQSQSP.TNWSPAV.IKKAKSPTPSPSPPRN.DQEGG
Retrocopy KPPAPPSPIQSQSPPTNWSPAVRIKKAKSPTPSPSPPRNLDQEGG

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	0.11 RPM	20.48 RPM
SRP051959_heart	0.12 RPM	27.43 RPM
SRP051959_kidney	0.11 RPM	36.34 RPM
SRP051959_liver	0.02 RPM	22.35 RPM
SRP051959_lung	0.11 RPM	32.60 RPM
SRP051959_lymph_node	0.02 RPM	35.34 RPM
SRP051959_skeletal_muscle	0.04 RPM	21.64 RPM
SRP051959_spleen	0.06 RPM	33.51 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1280 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1280 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1280 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013772	1 retrocopy	retro_btau_290,
Callithrix jacchus	ENSCJAG00000020822	2 retrocopies	retro_cjac_1280 , retro_cjac_3900,