RetrogeneDB ID: retro_btau_1834

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:90428766..90430808(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSRP1
• Ensembl ID: ENSBTAG00000000375
• Aliases: None
• Description: FACT complex subunit SSRP1 [Source:RefSeq peptide;Acc:NP_001094511]

Sequence

>retro_btau_1834
ATGGCAGAAACCCTCGAGTTCAATGATGTGTATCAGGAGGTGAAAGGCTCCATGAATGACAGTCGGCTGAGGTTGAACCG
CCAGGGCATCAACTTTAAGAACAGTAAGACGGGCAATGTGGACAACATCCAGGCCGGGGAGTTGACAGAAGGCATCTGGC
CCTGGGTAGCTCTGGGCCATGGGCTTAAACTGCTCATGAGGAATGGCCATGTCTACAAGTATGATGGCTTTGGAGAATCG
GAATTTGAGAAACTCTCTGATTTCTTAAAAACTCACTATTGCCTGGAGCTAATGGAGAAGGACCTATGTGTGAAGGGTTG
GAACTGGGGAACCGTGAAGTTTTGTGGGCAGCTGCTTTCCCTCGACATTGAAGACCAGCCAGTCTTCGAGATCCTTCTCA
GCAATGTGTCCCAGTACACCACAGGCAAGAATGGGGTGACACTGGAATTCCACCAGAATGATGACACGGAGGTCTCTCTC
ATGGAGGTGTGCTTCTAGGTGCCGCCCACCCAGGAAGACAGTGTGGACCCCGACGAGGCCTTCTCCCAGAATGTACTGTC
AAAGGCGGACGTGATGCAGGCCACCAGAGACGCCATCTGCATCTTCCGGGAGCTGCAGTGTCTGACTCCCTGAGGCCACT
GTAACATCCGCATCTACCCCACCTCCCTGCACCTGCACACAAGATCTTCGACTACAAGATCCCCTACACCATGGTGCTGC
GTCTCTTCCTGCTGCCCACAAGGACCAGCGCCAGATGTTCTTTGTGATCAGCCCGGACCCCCCCATCAAGCAGGGCCAGA
CCCGCTACCACTTCCTCATCCTCCTCTTCTCCAAGGATGAGGACTTCTCCTTGATGCTCAGCATGAACGAGGAGGAAGTG
GAGAAGCCCTTCGAGGGGCAGCTCACCAAGAACATGTTGGGATCCCTCTATGAGATGGTCAGCCAGGTCATGAAAGTGCT
GGTGAACCACAAGATCACAGTCCCCGACAACTTCTAAGGGCACTTGGGGGCCCAGTGCATCACCTGCTCCTACAAGGCCA
GCTCAGGGCTGTTGTACCCCCTGGAGCGGGGCTTTATCTACATCCACAGGCTGCCCATGCACACCTGCTTCGACGAGATC
TCCTTTGTCAACTTTGCCCATGGTACCACCACGACGCATTCCTTTGACTTTGAAATTGAGACCAAGCAGGGCACCCAGTA
TACTTTCAGCAGCATTGAGAGGGAAGAGTATGGAAAGCTGTTCGACTTTGTCAACGCCAAGAAACTCAGCATCAAAAACC
AAGGATTGAAAGAGGGCATGAACCCCAGCTACGATGAATATGCTGACTTGGAGGAAGACCAGCATGATGCCTACTTGGAG
TGGATGAAGGAGGAGGGCAAGATCCGGGAGGAGAATGCCAATGACAGCAACGATGACTCCAGAGAAGAGAGTGATGAGTC
ATTCAACCCAGGTGAAGAGGAGGAAGACGTGGCAGAGGAGTTTGACAGCAACGCCTCTGCCAGCTCCTCCAGTAATAGAG
GGTGACAGTGACCAGGCAGAGAAGAAACGGAAGCAGCTTAAAAAGGCCAAAATGGCCAAGGACTGCAAGAGCCGCAAGAA
GCCCATGGAGGTAAAGAAGGGCAGAGACCCTAATGCCCTCAAGAGGCCCATGTCTGCCTACATGCTGTGGCTCAATGCCA
GCTGAGAGAAGATCAAGTCAGACCATCTGGGCATCAGTATCATGGATCTCTCCAAGAAGGCTGGTGAAATCTGGAAGGGA
ATGCCCAAGGAGAAGAAAGAAGAGTGGGATCACAAGGCTGAGGATGTCAGGAGGGAATATGAAAAAGCCATAAAAGAATA
TGAAGGGGGCTGGGGAGAGTGCTCTAAGAGGGATAAGTCCAAGAAGAAGAAAGTCAAGGTGAAGATGGAGAAGAAATCCA
TACCCTCCAGGGGCTCATCATCGAAGTCTTCATCAAGGCAGCTGAGCGAGAGCTTCAAGAGCAAAGAGTTTGCGTCCAGT
GACGAGAGCTCTTCCAGAGAGAACAAGAGCAAAAAGAAGAGG

Alignment

ORF - retro_btau_1834 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.3 %
• Parental protein coverage: 96.19 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAETLEFNDVYQEVKGSMNDGRLRLSRQGIIFKNSKTGKVDNIQAGELTEGIWRRVALGHGLKLLTKNGH
          MAETLEFNDVYQEVKGSMND.RLRL.RQGI.FKNSKTG.VDNIQAGELTEGIW..VALGHGLKLL..NGH
Retrocopy MAETLEFNDVYQEVKGSMNDSRLRLNRQGINFKNSKTGNVDNIQAGELTEGIWPWVALGHGLKLLMRNGH

Parental  VYKYDGFRESEFEKLSDFFKTHYRLELMEKDLCVKGWNWGTVKFGGQLLSFDIGDQPVFEIPLSNVSQCT
          VYKYDGF.ESEFEKLSDF.KTHY.LELMEKDLCVKGWNWGTVKF.GQLLS.DI.DQPVFEI.LSNVSQ.T
Retrocopy VYKYDGFGESEFEKLSDFLKTHYCLELMEKDLCVKGWNWGTVKFCGQLLSLDIEDQPVFEILLSNVSQYT

Parental  TGKNEVTLEFHQNDDAEVSLMEVRFYVPPTQEDGVDPVEAFAQNVLSKADVIQATGDAICIFRELQCLTP
          TGKN.VTLEFHQNDD.EVSLMEV.F.VPPTQED.VDP.EAF.QNVLSKADV.QAT.DAICIFRELQCLTP
Retrocopy TGKNGVTLEFHQNDDTEVSLMEVCF*VPPTQEDSVDPDEAFSQNVLSKADVMQATRDAICIFRELQCLTP

Parental  RGRYDIRIYPTFLHLHG-KTFDYKIPYTTVLRLFLLP-HKDQRQMFFVISLDPPIKQGQTRYHFLILLFS
          .G...IRIYPT.LHLH..K.FDYKIPYT.VLRLFLLP.HKDQRQMFFVIS.DPPIKQGQTRYHFLILLFS
Retrocopy *GHCNIRIYPTSLHLHT<KIFDYKIPYTMVLRLFLLP<HKDQRQMFFVISPDPPIKQGQTRYHFLILLFS

Parental  KDEDISLTLNMNEEKVEKRFEGRLTKNMSGSLYEMVSRVMKALVNRKITVPGNFQGHSGAQCITCSYKAS
          KDED.SL.L.MNEE.VEK.FEG.LTKNM.GSLYEMVS.VMK.LVN.KITVP.NF.GH.GAQCITCSYKAS
Retrocopy KDEDFSLMLSMNEEEVEKPFEGQLTKNMLGSLYEMVSQVMKVLVNHKITVPDNF*GHLGAQCITCSYKAS

Parental  SGLLYPLERGFIYVHKPPVHIRFDEISFVNFARGTTTTRSFDFEIETKQGTQYTFSSIEREEYGKLFDFV
          SGLLYPLERGFIY.H..P.H..FDEISFVNFA.GTTTT.SFDFEIETKQGTQYTFSSIEREEYGKLFDFV
Retrocopy SGLLYPLERGFIYIHRLPMHTCFDEISFVNFAHGTTTTHSFDFEIETKQGTQYTFSSIEREEYGKLFDFV

Parental  NAKKLNIKNRGLKEGMNPSYDEYADSDEDQHDAYLERMKEEGKIREENANDSSDDSGEETDESFNPGEEE
          NAKKL.IKN.GLKEGMNPSYDEYAD..EDQHDAYLE.MKEEGKIREENANDS.DDS.EE.DESFNPGEEE
Retrocopy NAKKLSIKNQGLKEGMNPSYDEYADLEEDQHDAYLEWMKEEGKIREENANDSNDDSREESDESFNPGEEE

Parental  EDVAEEFDSNASASSSSN-EGDSDREEKKRKQLKKAKMAKDRKSRKKPLEVKKGKDPNAPKRPMSAYMLW
          EDVAEEFDSNASASSSSN.EGDSD..EKKRKQLKKAKMAKD.KSRKKP.EVKKG.DPNA.KRPMSAYMLW
Retrocopy EDVAEEFDSNASASSSSN>EGDSDQAEKKRKQLKKAKMAKDCKSRKKPMEVKKGRDPNALKRPMSAYMLW

Parental  LNASREKIKSDHPGISVTDLSKKAGEIWKGMSKEKKEEWDRKAEDARREYEKAMKEYEGGRGESSKRDKS
          LNAS.EKIKSDH.GIS..DLSKKAGEIWKGM.KEKKEEWD.KAED.RREYEKA.KEYEGG.GE.SKRDKS
Retrocopy LNAS*EKIKSDHLGISIMDLSKKAGEIWKGMPKEKKEEWDHKAEDVRREYEKAIKEYEGGWGECSKRDKS

Parental  KKKKKVKVKMEKKSTPSRGSSSKSSSRQLSESFKSKEFVSSDESSSGENKGKKKR
          .KKKKVKVKMEKKS.PSRGSSSKSSSRQLSESFKSKEF.SSDESSS.ENK.KKKR
Retrocopy -KKKKVKVKMEKKSIPSRGSSSKSSSRQLSESFKSKEFASSDESSSRENKSKKKR

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	0.00 RPM	24.08 RPM
ERP005899_muscle	0.00 RPM	127.22 RPM
SRP017611_brain	0.05 RPM	108.81 RPM
SRP017611_kidney	0.06 RPM	74.86 RPM
SRP017611_liver	0.00 RPM	50.59 RPM
SRP030211_testis	0.01 RPM	103.94 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1834 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1834 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1834 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
Bos taurus	ENSBTAG00000000375	1 retrocopy	retro_btau_1834 ,
Cavia porcellus	ENSCPOG00000000480	1 retrocopy	retro_cpor_70,
Equus caballus	ENSECAG00000016612	1 retrocopy	retro_ecab_516,