RetrogeneDB ID: retro_btau_290

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 1:4753764..4755609(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRRM1
• Ensembl ID: ENSBTAG00000013772
• Aliases: None
• Description: None

Sequence

>retro_btau_290
ATGGATGCAGGATTCTTCTGCGGAACAAGTGCAGAACAGGATAATCGGTTCAGCAACAAACAGAAGAAGCTACTGAAGCA
GCTGAAATTAGCAGAATGCCTAGGAAAAAAAGGTGGACATGAGCAAAGCAATTTTGGAGGTTATAAAGCCTTGTATAACA
AAACAAGTAATGAAAATCCTTGGGTTTGAAGATGATGTTGTGATTGAGTTTATATTCAATCAGCTGGAAGTGAAGAATCC
AGATTCAAAAATGATGCAAATCAACCTGACCAGGTTTTTGAATGGAAAAAATGCTAGGGAATTTACAGGAGAACTGTGGC
TCCTACTGTTAAATGCACAAGAAAACATCACTGGAATCCCTTCTGCTCTCCTAGAACTGAAGAAGGAAGAAATACAACAG
AGACAGATTGAACAAGAAAAGTTGGCATCTATGAAAAAGCAAAATGAAGACAAGGATAAGAGGGATAAAGAAGAAAAATA
AAGCAGAAGAGAAAACAGGGAGCCGTCTCAAAGCCCAAGAAGATGCAAATCCAGTTCTCCTTCCCCTCGAAGACGATCTT
TCCCTGTCAGGGGACAGAGAAAGCGCAGTCATTCTCTATCTCCCTGTCACAGAACCAAAAGCCGGAGTCCTTCCTCTGCT
CCAGAGAAGAAGGAAAAAATTCCAGAGCTCCCAGAGCCATCAGTGAAAGTAAAAGAACCGTCACTACAAGAGGCCACTTC
TACTAATGACATTCTGAAAGTTTCCAAGACTGAACCAGTACTAGAGCCTAAAGAACCTTCTCCGGAGAAAAACTCCAAAA
AGGAAAAGGAAAAGGAAAAACCCGGCCAAGATCTCGGTCATGTTCCAAGTCAAGATCCCAGACACGTTCTCGCTCTCCTT
CTCATACTAGACCAAGAAGGCACCATAGATCTCGGTCAAGATCATACTCACCTAAAAGACAGCCAAACCCAAGAAGAAGG
CCATCTCCTCTAAGAAGAACCCCACCGAGACGCATGCCTCCTCCACCAAGGCATAGGAGTAGATCTCCAGTGAGACGAAG
AAGGCATTCATCGGCATCCTTGTCTGGGAGTAGTTCATCATCTTCTTCGTCTAGTTCCCAGTCACCACCAAAGAAGCCTC
CGAAGAGGACATCTAGCCCTCCTCGAAAAACTCGTAGGTTATCTCCTTCAGCAAGTCCTCTGACGCGAAGGCATAGGCCA
TCACCTCCAGCTATTCCGCCGCCAAAAACTCGTCATTCCCGAACACCCCAGCAGTCAAACCATACAAGGAGAAGTCGTGT
TTCTGTCTCTCCAGGGAGAACTTCAGGTAAAGTGACAAAACATAAAGGTACTAAGAAAAGAGAATCCCCTTCACCAGCAC
CGAAGCCTCGGAAAGTAGAGTTATCTGAATCAGAAGAAGATAAAGGTGGCAAAATGGCTGCAGCAGATTCTGTGCTGCAG
AGACGCCAATATAGATGACAGAACCAGCAGTCTTCATCTTATTCTGGCTCCTCTTCCTCAGAAGATGAACGACCCAAAAG
GTCCCTTGTGAAGAATGGTGAGGTAGGCAGGCGACGGAGACATTCCCCTTCCTGGAGTGCCTCTCCATCACCTCGAAAGC
GCCAGAAAGAGGCTTCCCCTCATGGTAGACGGAGGAGAAGTCCCTCCCCACCTCCCTCCAGAAGGCGACGTTCTCCTTCT
CCTGCTCCTCCACCTCGTCGACACAGGTCTTCCACACCACCACCACGTCGAAGGACTCCGTCTCCTCCTCCATGTCGTCG
TTCACCTTCCCCAAGAAGATACTTTCCTCCAATACAGAGGAGAAACTCTCCTTCTCCACCTCCAAAGAGAAGAACGGCCT
CCCCC

Alignment

ORF - retro_btau_290 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.08 %
• Parental protein coverage: 68.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDAGFFRGTSAEQDNRFSNKQKKLLKQLKFAECL-EKKVDMSKVNLEVIKPWITKRVTEILGFEDDVVIE
          MDAGFF.GTSAEQDNRFSNKQKKLLKQLK.AECL.EKKVDMSK..LEVIKP.ITK.V..ILGFEDDVVIE
Retrocopy MDAGFFCGTSAEQDNRFSNKQKKLLKQLKLAECL>EKKVDMSKAILEVIKPCITKQVMKILGFEDDVVIE

Parental  FIFNQLEVKNPDSKMMQINLTGFLNGKNAREFMGELWPLLLSAQENIAGIPSAFLELKKEEIKQRQIEQE
          FIFNQLEVKNPDSKMMQINLT.FLNGKNAREF.GELW.LLL.AQENI.GIPSA.LELKKEEI.QRQIEQE
Retrocopy FIFNQLEVKNPDSKMMQINLTRFLNGKNAREFTGELWLLLLNAQENITGIPSALLELKKEEIQQRQIEQE

Parental  KLASMKKQDEDKDKRDKEEKESSREKRERSRSPRRRKSRSPSPRRRSSPVRRERKRSHSRSPRHRTKSRS
          KLASMKKQ.EDKDKRDKEEK.S.RE.RE.S.SPRR.KS.SPSPRRRS.PVR..RKRSHS.SP.HRTKSRS
Retrocopy KLASMKKQNEDKDKRDKEEK*SRRENREPSQSPRRCKSSSPSPRRRSFPVRGQRKRSHSLSPCHRTKSRS

Parental  PSPAPEKKEKTPELPEPSVKVKEPSVQEATSTSDILKVPKTEPVLEPKEPSPEKNSKKEKEKTRP-RSRS
          PS.APEKKEK.PELPEPSVKVKEPS.QEATST.DILKV.KTEPVLEPKEPSPE...........P.R.RS
Retrocopy PSSAPEKKEKIPELPEPSVKVKEPSLQEATSTNDILKVSKTEPVLEPKEPSPEXXXXXXXXXXXP<RPRS

Parental  R--SKSRSRTRSRSPSHTRPRKRHRSRSRSYSPRRRPSPRRRPSPRRRTPPRRMPPPPRHRRSRSPVRRR
          R..SKSRS.TRSRSPSHTRPR..HRSRSRSYSP.R.P.PRRRPSP.RRTPPRRMPPPPRH.RSRSPVRRR
Retrocopy RSCSKSRSQTRSRSPSHTRPRRHHRSRSRSYSPKRQPNPRRRPSPLRRTPPRRMPPPPRH-RSRSPVRRR

Parental  RRSSASLSGSSSSSSSSRSRSPPKKPPKRTSSPPRKTRRLSPSASPPRRRHRPSPPATPPPKTRHSPTPQ
          R.SSASLSGSSSSSSSS.S.SPPKKPPKRTSSPPRKTRRLSPSASP..RRHRPSPPA.PPPKTRHS.TPQ
Retrocopy RHSSASLSGSSSSSSSSSSQSPPKKPPKRTSSPPRKTRRLSPSASPLTRRHRPSPPAIPPPKTRHSRTPQ

Parental  QSNRTRKSRVSVSPGRTSGKVTKHKGTEKRESPSPAPKPRKVELSESEEDKGGKMAAADSVQQRRQYRRQ
          QSN.TR.SRVSVSPGRTSGKVTKHKGT.KRESPSPAPKPRKVELSESEEDKGGKMAAADSV.QRRQYR.Q
Retrocopy QSNHTRRSRVSVSPGRTSGKVTKHKGTKKRESPSPAPKPRKVELSESEEDKGGKMAAADSVLQRRQYR*Q

Parental  NQQSSSDSGSSSSSEDERPKRSHVKNGEVGRRRRHSPSRSASPSPRKRQKEASPRGRRRRSPSPPPARRR
          NQQSSS.SG.SSSSEDERPKRS.VKNGEVGRRRRHSPS.SASPSPRKRQKEASP.GRRRRSPSPPP.RRR
Retrocopy NQQSSSYSG-SSSSEDERPKRSLVKNGEVGRRRRHSPSWSASPSPRKRQKEASPHGRRRRSPSPPPSRRR

Parental  RSPSPAPPPRRRRSPTPPPRRRTPSPPPRRRSPSPRRYSPPIQRRYSPSPPPKRRTASP
          RSPSPAPPPRR.RS.TPPPRRRTPSPPP.RRSPSPRRY.PPIQRR.SPSPPPKRRTASP
Retrocopy RSPSPAPPPRRHRSSTPPPRRRTPSPPPCRRSPSPRRYFPPIQRRNSPSPPPKRRTASP

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
ERP005899_liver	0.07 RPM	40.81 RPM
ERP005899_muscle	0.05 RPM	60.39 RPM
SRP017611_brain	0.05 RPM	86.15 RPM
SRP017611_kidney	0.06 RPM	106.27 RPM
SRP017611_liver	0.00 RPM	60.86 RPM
SRP030211_testis	0.01 RPM	148.97 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_290 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_290 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_290 has 0 orthologous retrocopies within eutheria group .

---

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,