RetrogeneDB ID: retro_pabe_2139

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:92695550..92697202(-)
• Located in intron of: ENSPPYG00000013073

Retrocopy information

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

Parental gene information

• Parental gene symbol: SCYL2
• Ensembl ID: ENSPPYG00000004865
• Aliases: None
• Description: SCY1-like 2 (S. cerevisiae) [Source:HGNC Symbol;Acc:19286]

Sequence

>retro_pabe_2139
TTGACTTCAGAATTTGTAAACCCTGACATGGTACCTTTTGTTTTGCCCAGTGTTCTGCTGATCGTTGAGGAATGCACCAA
AGAAGAATATGTCAAATTAATTCCACCTGAACTTGGCCCTGTGTTTAAGCAGCAGGAGCCAATCCAGATTTTGTTAATTT
TCCTACAAAAAATGGATTTGCTACTAACCAAAACCCCTCCCAATGAGATAAAGAACAGTGTTCTACCCATGGTTTACAGA
GCACTAGAAGCTCCTTCCATTCAGTACCAGGAGCTCTGTCTAAACATCATTCCAACCTTTGCAAATCTTATAGACTACCC
ATCATGAAACATACTTTGATACCAAGAATTAAAAATGTCTGTCTACAAACGTCTTCCCTTGCTTTTCCTGTAAATTCATT
AGTGTGCTTAGGAAAGATTTTGGAATACTTGGATAAGTGGTTTGTACTTGATGATATCCTACCCTTCTTAGAACAAATTC
CATCCAAAGAGTCTGCAGTCCTCATGGGTATTTTAGGCATTTACTAATGTACTTTTACTCATAAGTTGGGAATCACCAAA
GAGCAGCTGACTGGAAAAGTATTGCCTCATCTTATTCCCCTGAGTATTGAAAACAATCTTAACCAGTTCAATTCTTTCAT
TTCCATCATAAAAGAGATGCTGAATAGATTGGAGTCTGAACATAAGACTAAGCTGGAGCAACTTCACATAATGCAAGAAC
AACAGAAATCTTTGGACATAGGAAATGAAATGAATGTTTCTGAGGAGACAAAAGTTACAAATATTGGGAATCAGCAAATT
GACAAGGTTTTTAACCACATTGGAGCAGACCTTCTGACTGGCAGTGATTCCGAAAATAAAGAGGATGGGTTTCAGAATAA
ACATAAAAGAGCATCACTTACACTTGAAGAAAAACAAAAATTAGCAAGAGAACAAGAGCAGGCATAGAAGTTGAAAAGCC
AGCAGCCTCTTAAACCCCAAGTGTACACACCTATTGCTGCTGTTAAACAGACTAAGGACTTGACAGACACATTGATGGAT
AATATGTCATCTTTGACTAGCCTTTCTGTGAGTACCCCTAAACCTTCTGCTTCAAGTACGTTCACTTCTGTTCCTTCCAT
GGGCATTGGCATGATGTTTTCTACACCAGTTGATAATACAAAGAGAAATTTGACAAATGGCCTAAATGCCAATATGGGCT
TTCAGACTTCAGGATTCAACATGCCCGTTACTACAAACCAGAACTTCTACAGTAGTCCAAGCACGGTTGGGAGTGACCAA
AATGACTCTGGAACACCTCCCACTTTGCCAAACTTCAGTGCTTTGAATGTTCCTCCTGCTGGTGCGAAGCCGACCCAACA
AAGACCCACAGATATGTCTGCCCTTAATAATCTCTTTGGCCCTCAGAAACCCGAAGTTAGCATGAACCAATTATCACAAC
AGAAACCAAATCAGTGGCTTAATCAGTTTGTACCTTCTCAAGGTTCTCCAGCTACGGGCAGTTCAGTAATGGGAACACAG
ATGAACATGATAGGACAATCTGCCTTTGGTACATAGGGTAATCCTTTCTTCAACCCACAGAACTTTGCATAGCCACCAAC
TGCTATGACCAATAGCAGTTCAGCTAGCAATGATTTAAAAGATCTTTTTGGG

Alignment

ORF - retro_pabe_2139 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.74 %
• Parental protein coverage: 59.96 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LTSEFVNPDMVPFVLPNVLLIAEECTKEEYVKLILPELGPVFKQQEPIQILLIFLQKMDLLLTKTPPDEI
          LTSEFVNPDMVPFVLP.VLLI.EECTKEEYVKLI.PELGPVFKQQEPIQILLIFLQKMDLLLTKTPP.EI
Retrocopy LTSEFVNPDMVPFVLPSVLLIVEECTKEEYVKLIPPELGPVFKQQEPIQILLIFLQKMDLLLTKTPPNEI

Parental  KNSVLPMVYRALEAPSIQIQELCLNIIPTFANLIDYPS-MKNALIPRIKNACLQTSSLAVRVNSLVCLGK
          KNSVLPMVYRALEAPSIQ.QELCLNIIPTFANLIDYPS.MK..LIPRIKN.CLQTSSLA..VNSLVCLGK
Retrocopy KNSVLPMVYRALEAPSIQYQELCLNIIPTFANLIDYPS<MKHTLIPRIKNVCLQTSSLAFPVNSLVCLGK

Parental  ILEYLDKWFVLDDILPFLQQIPSKEPAVLMGILGIYKCTFTHKKLGITKEQLAGKVLPHLIPLSIENNLN
          ILEYLDKWFVLDDILPFL.QIPSKE.AVLMGILGIY.CTFTHK.LGITKEQL.GKVLPHLIPLSIENNLN
Retrocopy ILEYLDKWFVLDDILPFLEQIPSKESAVLMGILGIY*CTFTHK-LGITKEQLTGKVLPHLIPLSIENNLN

Parental  LNQFNSFISVIKEMLNRLESEHKTKLEQLHIMQEQQKSLDIGNQMKVSEETKVTNIGNQQIDKVFNNIGA
          ..QFNSFIS.IKEMLNRLESEHKTKLEQLHIMQEQQKSLDIGN.M.VSEETKVTNIGNQQIDKVFN.IGA
Retrocopy --QFNSFISIIKEMLNRLESEHKTKLEQLHIMQEQQKSLDIGNEMNVSEETKVTNIGNQQIDKVFNHIGA

Parental  DLLTGSESENKEDGLQNKHKRASLTLEEKQKLAKEQEQAQKLKSQQPLKPQVHTPVATVKQTKDLTDTLM
          DLLTGS.SENKEDG.QNKHKRASLTLEEKQKLA.EQEQA.KLKSQQPLKPQV.TP.A.VKQTKDLTDTLM
Retrocopy DLLTGSDSENKEDGFQNKHKRASLTLEEKQKLAREQEQA*KLKSQQPLKPQVYTPIAAVKQTKDLTDTLM

Parental  DNMSSLTSLSVSTPKSSASSTFTSVPSMGIGMMFSTPTDNTKRNLTNGLNANMGFQTSGFNMPVNTNQNF
          DNMSSLTSLSVSTPK.SASSTFTSVPSMGIGMMFSTP.DNTKRNLTNGLNANMGFQTSGFNMPV.TNQNF
Retrocopy DNMSSLTSLSVSTPKPSASSTFTSVPSMGIGMMFSTPVDNTKRNLTNGLNANMGFQTSGFNMPVTTNQNF

Parental  YSSPSTV-GVTKMTL-GTPPTLPNFNALSVPPAGAKQTQQRPTDMSALNNLFGPQKPKVSMNQLSQQKPN
          YSSPSTV.GVTKMTL.GTPPTLPNF.AL.VPPAGAK.TQQRPTDMSALNNLFGPQKP.VSMNQLSQQKPN
Retrocopy YSSPSTV>GVTKMTL<GTPPTLPNFSALNVPPAGAKPTQQRPTDMSALNNLFGPQKPEVSMNQLSQQKPN

Parental  QWLNQFVPPQGSPAMGSSVMGTQMNVIGQSTFGMQGNPFFNPQNFAQPPTTMTNSSSASNDLKDLFG
          QWLNQFVP.QGSPA.GSSVMGTQMN.IGQS.FG..GNPFFNPQNFA.PPT.MTNSSSASNDLKDLFG
Retrocopy QWLNQFVPSQGSPATGSSVMGTQMNMIGQSAFGT*GNPFFNPQNFA*PPTAMTNSSSASNDLKDLFG

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_prefrontal_cortex	0.22 RPM	13.33 RPM
SRP007412_cerebellum	0.12 RPM	22.98 RPM
SRP007412_heart	0.00 RPM	11.71 RPM
SRP007412_kidney	0.03 RPM	16.47 RPM
SRP007412_liver	0.00 RPM	15.94 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2139 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2139 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2139 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,