RetrogeneDB ID: retro_mmul_957

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 12:65164535..65166337(-)
• Located in intron of: ENSMMUG00000023812

Retrocopy information

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

Parental gene information

• Parental gene symbol: SCYL2
• Ensembl ID: ENSMMUG00000023600
• Aliases: None
• Description: SCY1-like protein 2 [Source:RefSeq peptide;Acc:NP_001253819]

Sequence

>retro_mmul_957
CAGATTCCCTTCTTTGATGATGTTGGTGCAGTAACACTGCAATGTTTTAATACCTTTTTCCAAAGAGATTATCTTCAGAA
ATCACAGTTTTTCAACAGACTGTCAAAGGTTCTACTGCCCAAGCATGTCATTGTGCAGAGAATTTTGACTTGTTTGACTT
CAGAATTTGTAAACCCTGACATGGTACCTTTTGTTTTGCCCAGTGTTCTACTGATCATTGAGGAATGCACCAAAGAAGAA
TATGTCAAATTAATTCCACCTGAACTTGGTCCTGTGTTTAAGCAGCAGGAGCCAATCCAGATTTTGGTAATTTTCCGACA
AAAAATGGATTTGCTACTAACCAGAACCCCTCCCGATGAGATAAAGAACAGTGTTCTACCCATGGTTTACAGAGCACTAG
AAGCTCCTTCCATTCAGACCCAGGAGCTCTGTCTAAACATCATTCCAGCCTTTGCAAATCTTATAGACTACCCATCCATG
AAACGTACTTTGATACCAAGAATTAAAATGCCTGTCTACAAATGTCTTCCCTTGCTGTTTGTGTAAATTCATTAGTGTGC
TTATGAAAGATTTTGGAATACTTGGATAAGTGGTTTGTACTTGATGATAGCCTACCCTTCTTACAACAAATTTCATCCAA
AGAATCTGCAGTCTTCATGGGTATTTTAGGCATTTACAAATGTACTTTTACTCATAAGTTGGGAATCACCAAAGAGCAGC
TGGCTGAATAAGTATTGCCTCATCTTATTCCCCTGAGTATTGAAAACAATCTTAATCAGTTCAATTCTTTCATTTCCATC
ATAAAAGAGATGCTTAATAGATTGGAGTCTGAACATAAGACTAAGCTGGAACAACTTCATATAATGCAAGAACAGCAGAA
ATCTTTGGACATAGGAAATCAAATTAATGTTTCTGGGGAGACAAAAGTTACAAATATTTTGAATCAGCAAATTGACAAGG
TTGTTAACCACATTGGAGCAGACCTTCTGACTGGCAGTGATTCCAAAAATAAAGAGGATGGGTTACAGAATAAACATAAA
ACAGCATCACTTACATTTGAAGAAAAACAAAAATTAGCAAAAGAACAAGAGCAGGCACAGAAGTTGAAAAGCCAGCAGCC
TCTTAAACCCCAATGCATACACCTATTGCTACTGTTAAACAGAGTAATGACTTGACAGACACATTGATGGATAATATGTC
ATCTTCGACTAGCCTTTCTGTTAGTACCCCTAAACCTTCTGCTTCAAGTACTTTCACTTCTCTTCCTTCCATGGGCATTG
GCATGATGTTTTCTATACCAGTTGATAATACAAAGAAAAATTTGACAAATGGCCTAAATGCCAATATGGGCTTTCAGACT
TCAGGATTCAACATGCCTGTTACTACAAACCAGAACTTCTACAGTAGTCCAAGCACAGATGGAGTGACCAAGATGACTCT
GGAACCCCTCCCACTTTGCCAAACTTCAGTGCTTTGAATGTTCCTCCTGCTGGTGCAAAGCCGACCCAACAAAGACCCAC
AGATATGTCTGCCCTTAATAATCTCTTTGGCCCTCAGAAACCCAAAGTTAGCATGAACCAGTTATCACAACAGAAACCAA
ATCAGTGGCTCAATCAGTTTGTACCTCCTCAAGGTTCTCCAGCTATGGGCATTCAGTAATGGGAACACAGATGAACATGA
TAGGACAATCTGCCTTTGGTACGCAGGGTAATCCTTTCTTCAACCCACGGAACTTTGCATAGCCACCAACTACTATGACC
AATAGCAGTTCAGCTAGCAGTGATTTAAAAGATCTTTTTGGG

Alignment

ORF - retro_mmul_957 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.05 %
• Parental protein coverage: 65.34 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KIPFFDDVGAVTLQYFDTLFQRDNLQKSQFFKGLPKVLPKLPKRVIVQRILPCLTSEFVNPDMVPFVLPN
          .IPFFDDVGAVTLQ.F.T.FQRD.LQKSQFF..L.KVL..LPK.VIVQRIL.CLTSEFVNPDMVPFVLP.
Retrocopy QIPFFDDVGAVTLQCFNTFFQRDYLQKSQFFNRLSKVL--LPKHVIVQRILTCLTSEFVNPDMVPFVLPS

Parental  VLLIAEECTKEEYVKLILPELGPVFKQQEPIQILLIFLQKMDLLLTKTPPDEIKNSVLPMVYRALEAPSI
          VLLI.EECTKEEYVKLI.PELGPVFKQQEPIQIL.IF.QKMDLLLT.TPPDEIKNSVLPMVYRALEAPSI
Retrocopy VLLIIEECTKEEYVKLIPPELGPVFKQQEPIQILVIFRQKMDLLLTRTPPDEIKNSVLPMVYRALEAPSI

Parental  QIQELCLNIIPTFANLIDYPSMKNALIPRIK-NACLQTSSLAVRVNSLVCLGKILEYLDKWFVLDDILPF
          Q.QELCLNIIP.FANLIDYPSMK..LIPRIK.NACLQ.SSLAV.VNSLVCL.KILEYLDKWFVLDD.LPF
Retrocopy QTQELCLNIIPAFANLIDYPSMKRTLIPRIK<NACLQMSSLAVCVNSLVCL*KILEYLDKWFVLDDSLPF

Parental  LQQIPSKEPAVLMGILGIYKCTFTHKKLGITKEQLAGKVLPHLIPLSIENNLNLNQFNSFISVIKEMLNR
          LQQI.SKE.AV.MGILGIYKCTFTH.KLGITKEQLA..VLPHLIPLSIEN..NLNQFNSFIS.IKEMLNR
Retrocopy LQQISSKESAVFMGILGIYKCTFTH-KLGITKEQLAE*VLPHLIPLSIEN--NLNQFNSFISIIKEMLNR

Parental  LESEHKTKLEQLHIMQEQQKSLDIGNQMNVSEEAKVTNTGNQQIDKVFNNIGADLLTGSESENKEDGLQN
          LESEHKTKLEQLHIMQEQQKSLDIGNQ.NVS.E.KVTN..NQQIDKV.N.IGADLLTGS.S.NKEDGLQN
Retrocopy LESEHKTKLEQLHIMQEQQKSLDIGNQINVSGETKVTNILNQQIDKVVNHIGADLLTGSDSKNKEDGLQN

Parental  KHKRASLTLEEKQKLAKEQEQAQKLKSQQPLKPQ-VHTPVATVKQTKDLTDTLMDNMSSLTSLSVSTPKS
          KHK.ASLT.EEKQKLAKEQEQAQKLKSQQPLKPQ..HTP.ATVKQ..DLTDTLMDNMSS.TSLSVSTPK.
Retrocopy KHKTASLTFEEKQKLAKEQEQAQKLKSQQPLKPQ<MHTPIATVKQSNDLTDTLMDNMSSSTSLSVSTPKP

Parental  SASSTFTSIPSMGIGMMFSTPTDNTKRNLTNGLNANMGFQTSGFNMPVNTNQNFYSSPSTVGVTKMTL-G
          SASSTFTS.PSMGIGMMFS.P.DNTK.NLTNGLNANMGFQTSGFNMPV.TNQNFYSSPST.GVTKMTL.G
Retrocopy SASSTFTSLPSMGIGMMFSIPVDNTKKNLTNGLNANMGFQTSGFNMPVTTNQNFYSSPSTDGVTKMTL<G

Parental  TPPTLPNFNALSVPPAGAKQSQQRPTDMSALNNLFGPQKPKVSMNQLSQQKPNQWLNQFVPPQGSPAM-G
          TPPTLPNF.AL.VPPAGAK..QQRPTDMSALNNLFGPQKPKVSMNQLSQQKPNQWLNQFVPPQGSPAM.G
Retrocopy TPPTLPNFSALNVPPAGAKPTQQRPTDMSALNNLFGPQKPKVSMNQLSQQKPNQWLNQFVPPQGSPAM<G

Parental  SSVMGTQMNVIGQSAFGMQGNPFFNPQNFAQPPTTMTSSSSASNDLKDLFG
          .SVMGTQMN.IGQSAFG.QGNPFFNP.NFA.PPTTMT.SSSAS.DLKDLFG
Retrocopy HSVMGTQMNMIGQSAFGTQGNPFFNPRNFA*PPTTMTNSSSASSDLKDLFG

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
SRP007412_brain	0.56 RPM	33.73 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	20.71 RPM
SRP007412_cerebellum	0.26 RPM	36.48 RPM
SRP007412_heart	0.18 RPM	11.84 RPM
SRP007412_kidney	0.82 RPM	26.76 RPM
SRP007412_liver	0.00 RPM	10.45 RPM
SRP007412_testis	0.04 RPM	57.29 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_957 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_957 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_957 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000136021	1 retrocopy	retro_hsap_2369,
Gorilla gorilla	ENSGGOG00000002948	1 retrocopy	retro_ggor_1799,
Macaca mulatta	ENSMMUG00000023600	1 retrocopy	retro_mmul_957 ,
Pongo abelii	ENSPPYG00000004865	1 retrocopy	retro_pabe_2139,
Sarcophilus harrisii	ENSSHAG00000011140	1 retrocopy	retro_shar_569,