RetrogeneDB ID: retro_cjac_3900

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286146.1:13901..16339(-)
• 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_3900
ATGGACGCGGGATTCTTCCGCGGAACATGTGCAGAACAGGATAATCGGTTCAGCGACAAACAGAAGAAACTACTGAAGCA
GCTGAAATTTGCAGAATGCCTAGAAAAAAAGGTGGGCACGAGCAAAGTAAATTTGGAAGTTATAAAGCCTTGGATAACAA
AAAGAGTAACGGAAATCCGTGGGTTTAAAGATGATGTTGTGATTGAGTTTATATTCAACCAGCTGGAAGTGAAGAATCCA
GACTACAAAATGATGCAAATCAACCTGACTGGATTTTTAAACGGAAAAAATGCTCGAGAATTTATGGGAGAACTGTGGCC
CCTGCTGCTAAGTGCACAAGAAAACGTCGCGGGAATCCCTTCTGCTTTCCTAGAGCTGAAGAAAGAAGAAATAAAACAAA
GACAGATTGAACAAGAAAAATGGGCATTTATGAAAAAGCAAGATGAAGACAAAGATAAAAGGGATAAGGAAGAGAAAGAA
AGCAGCAGAGAAAAAAGGGAGAGGTCTCGTAGCCCAAGAAGACGCAAATCCAGATCTCCTTCCCCTAGAAGACGACCTTC
CCCTGTCAGGAGAGAGAGAAAGCGCAGTCATTCTCGATCTCCCGGTCACAGAACCAAGAGCCGGAGTCCTTCCCCTGCTC
CAGAAAAGAAGGAAAAAACTCCAGAGCTCCCAGAACCTTCAGTGAAAGTAAAAGAACCTTCAGTACAAGAGGCCACTTCT
ACTAGTGACATTCTGAAAGTTCCCAAACCTGAACCTGTACCAGAGCCTAAAGAACCTTCTGCAGAAAAAAATTCCAAAAA
AGAAAAGGAGAAGGAAAAGACCCGACCACGATCTCGGTCACGCTCCAAATCAAGATCCTGGACGCGGTCCCGCTCTCCTT
CTCACACTCGACCTAGATGGCACCATAGGTCTCGATCGAGATCATATTCACCTAGAAGGTGGCCAAGCCCAAGAAGGCGG
CCATCTCCTCGAAGAAGAACTCCACCAAGGAGAATGCCTCCTCCACCAAGGCATAGAAGCAGCAGATCACCAGTAAGACG
AAGAAGACGTTCGTCAGCATCCTTGTCTGGGAGTAGCTCATCATCCTCTTCATCTCGTTCCCGGTCACCACCAAAGAAAC
CGCCCAAGAGGACATCCAGCCCCCTTCGAAAAACTCGTAGGTTATCTCCTTCAGCAAGTCCTCTAAGGCGAAGGCACAGG
CCATCACCTCCTGCAACTCCACCACCCCAAACTCGGCATTCCCCAACACCCCAGCAGTCAAACTGTACAAGAAAAAGTCG
TGTTTCCATGTCTCCAGGGAGAACATCAGTAACAAAACATAAAGGTACTGAGAAAAGAGAATCCCCTTCACCAGCACCGA
AGCCTAGAAAAGTAGAGTTATCTAAATCGGAAGAAGATAAAGGTGGCAAAATGGCTGCAGCAGATTCTGTGCAGCAGAGA
CGCCAATACCGACGACAAAACCAGCAGTCTTCATCTGACTCTGGCTCCTCCTCCTCCTCACAAGATGAAAGACCCAAGAG
ATCCCATGTGAAGAATGGTGAGGTTGGCAGGCGGCGGAGACATTCCCCTTCCCAGAGTGCCTCTCCATCACCACGACAGC
GCCAAAAAGAGACTTCCCCTCGGATGCAGATGGGAAAGCGATGGCAATCGCCAGTGACTAAAAGTGGTAGACGGAGGAGA
AGTCCAACCCCACCACCCACCAGAAGGCGACGGTCTCCTTCGCCCACCCCTCCTCCTCGACAGCGCAGGTCTCCCACACC
ACCACCACGACGAAGGACTCCTTCTCCACCTCCACGTCGGCGCTCACCTTCTCCTAGAAGATATTCTCCTCCAATACAGA
GGAGATACTCTCCTTCTCCACCTCCAAAGAGAAGAACGGCTTCTCCTCCTCCCCCTCCTAAACGAAGCGCATCACCATCT
CCATCACCAAAGCATCAGGTCTCCCATTCTCCACCTCCCAAACAAAGAAGCTCCCCAGTCACCAAGAGACGTTCACCTTC
ATTATCATCCAAGCATAGGAAAGGGTCTTCCCCAAGCCGGTCTATGCGGGAGGCCCGATCACCACAACCAAACAAACGGC
ATTTGCCCTCACCACGGCCTCCAGCTCCTCAGACCTCCTCAAGTCCTCCACCTGTTCGAAGAGGAGCGTCCTCATCACCC
CAAAGAAGACAGTCCCCATCTCCAAGTACTAGGCCCATTAGGAGAGTCGCCAGGACTCCGGAACCTAAAAAGATAAAAAA
GGCTGCTTCACCAAGCCCACAGTCTGTAACAGGGTCTCATCCTCCCGATCTGTCTCTGGGTCTCCTGAGCCAACAGTTAA
AAAGCCCCCAGCACCTCCGTCCCCCATCCAGTCTCAGTCACCGCCTACAAACTGGTCACCAGCTGTACGGATCAAAAAGG
CCAAAAGCCCGACACCAAGCCCATCACCGCCAAGAAAT

Alignment

ORF - retro_cjac_3900 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.92 %
• Parental protein coverage: 88.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDAGFFRGTSAEQDNRFSNKQKKLLKQLKFAECLEKKVDMSKVNLEVIKPWITKRVTEILGFEDDVVIEF
          MDAGFFRGT.AEQDNRFS.KQKKLLKQLKFAECLEKKV..SKVNLEVIKPWITKRVTEI.GF.DDVVIEF
Retrocopy MDAGFFRGTCAEQDNRFSDKQKKLLKQLKFAECLEKKVGTSKVNLEVIKPWITKRVTEIRGFKDDVVIEF

Parental  IFNQLEVKNPDSKMMQINLTGFLNGKNAREFMGELWPLLLSAQENIAGIPSAFLELKKEEIKQRQIEQEK
          IFNQLEVKNPD.KMMQINLTGFLNGKNAREFMGELWPLLLSAQEN.AGIPSAFLELKKEEIKQRQIEQEK
Retrocopy IFNQLEVKNPDYKMMQINLTGFLNGKNAREFMGELWPLLLSAQENVAGIPSAFLELKKEEIKQRQIEQEK

Parental  LASMKKQDEDKDKRDKEEKESSREKRERSRSPRRRKSRSPSPRRRSSPVRRERKRSHSRSPRHRTKSRSP
          .A.MKKQDEDKDKRDKEEKESSREKRERSRSPRRRKSRSPSPRRR.SPVRRERKRSHSRSP.HRTKSRSP
Retrocopy WAFMKKQDEDKDKRDKEEKESSREKRERSRSPRRRKSRSPSPRRRPSPVRRERKRSHSRSPGHRTKSRSP

Parental  SPAPEKKEKTPELPEPSVKVKEPSVQEATSTSDILKVPKPEPVPEPKEPSPEKNSKKEKEKEKTRPRSRS
          SPAPEKKEKTPELPEPSVKVKEPSVQEATSTSDILKVPKPEPVPEPKEPS.EKNSKKEKEKEKTRPRSRS
Retrocopy SPAPEKKEKTPELPEPSVKVKEPSVQEATSTSDILKVPKPEPVPEPKEPSAEKNSKKEKEKEKTRPRSRS

Parental  RSKSRSRTRSRSPSHTRPRRRHRSRSRSYSPRRRPSPRRRPSPRRRTPPRRMPPPPRHRRSRSPVRRRRR
          RSKSRS.TRSRSPSHTRPR..HRSRSRSYSPRR.PSPRRRPSPRRRTPPRRMPPPPRHR.SRSPVRRRRR
Retrocopy RSKSRSWTRSRSPSHTRPRWHHRSRSRSYSPRRWPSPRRRPSPRRRTPPRRMPPPPRHRSSRSPVRRRRR

Parental  SSASLSGSSSSSSSSRSRSPPKKPPKRTSSPPRKTRRLSPSASPPRRRHRPSPPATPPPKTRHSPTPQQS
          SSASLSGSSSSSSSSRSRSPPKKPPKRTSSP.RKTRRLSPSASP.RRRHRPSPPATPPP.TRHSPTPQQS
Retrocopy SSASLSGSSSSSSSSRSRSPPKKPPKRTSSPLRKTRRLSPSASPLRRRHRPSPPATPPPQTRHSPTPQQS

Parental  NRTRKSRVSVSPGRTSGKVTKHKGTEKRESPSPAPKPRKVELSESEEDKGGKMAAADSVQQRRQYRRQNQ
          N.TRKSRVS.SPGRTS..VTKHKGTEKRESPSPAPKPRKVELS.SEEDKGGKMAAADSVQQRRQYRRQNQ
Retrocopy NCTRKSRVSMSPGRTS--VTKHKGTEKRESPSPAPKPRKVELSKSEEDKGGKMAAADSVQQRRQYRRQNQ

Parental  QSSSDSGSSSSSEDERPKRSHVKNGEVGRRRRHSPSRSASPSPRKRQKETSPRMQMGKRWQSPVTKRFSG
          QSSSDSGSSSSS.DERPKRSHVKNGEVGRRRRHSPS.SASPSPR.RQKETSPRMQMGKRWQSPVTK..SG
Retrocopy QSSSDSGSSSSSQDERPKRSHVKNGEVGRRRRHSPSQSASPSPRQRQKETSPRMQMGKRWQSPVTK--SG

Parental  RRRRSPTPPPTRRRRSPSPAPPPRRRRSPTPPPRRRTPSPPPRRRSPSPRRYSPPIQRRYSPSPPPKRRT
          RRRRSPTPPPTRRRRSPSP.PPPR.RRSPTPPPRRRTPSPPPRRRSPSPRRYSPPIQRRYSPSPPPKRRT
Retrocopy RRRRSPTPPPTRRRRSPSPTPPPRQRRSPTPPPRRRTPSPPPRRRSPSPRRYSPPIQRRYSPSPPPKRRT

Parental  ASPPPPPKRRASPSPPPKHRVSHSPPPKQRSSPVTKRRSPSLSSKHRKGSSPSRSTREARSPQPNKRHSP
          ASPPPPPKR.ASPSP.PKH.VSHSPPPKQRSSPVTKRRSPSLSSKHRKGSSPSRS.REARSPQPNKRH.P
Retrocopy ASPPPPPKRSASPSPSPKHQVSHSPPPKQRSSPVTKRRSPSLSSKHRKGSSPSRSMREARSPQPNKRHLP

Parental  SPRPRAPQTSSSPPPVRRGTSSSPQRRQSPSPSTRPIRRVSRTPEPKKIKKGMLPKETGDVIGHVSRINQ
          SPRP.APQTSSSPPPVRRG.SSSPQRRQSPSPSTRPIRRV.RTPEPKKIKK...P........H......
Retrocopy SPRPPAPQTSSSPPPVRRGASSSPQRRQSPSPSTRPIRRVARTPEPKKIKKAASPSPQSVTGSHPPDLSL

Parental  QSKWSRAASPSPQSIRRVSS-SRSVSGSPEPAVKKPPAPPSPIQSQSPSTN
          ........SP..Q..R..SS.S.S......PAV....A..SP..S.SP..N
Retrocopy GLLSQQLKSP--QHLRPPSS<SQSPPTNWSPAVRIKKA-KSPTPSPSPPRN

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	0.04 RPM	20.48 RPM
SRP051959_heart	0.07 RPM	27.43 RPM
SRP051959_kidney	0.07 RPM	36.34 RPM
SRP051959_liver	0.15 RPM	22.35 RPM
SRP051959_lung	0.13 RPM	32.60 RPM
SRP051959_lymph_node	0.11 RPM	35.34 RPM
SRP051959_skeletal_muscle	0.02 RPM	21.64 RPM
SRP051959_spleen	0.08 RPM	33.51 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3900 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3900 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3900 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 ,