RetrogeneDB ID: retro_ggor_1799

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2b:89867032..89868581(-)
• Located in intron of: ENSGGOG00000003014

Retrocopy information

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

Parental gene information

• Parental gene symbol: SCYL2
• Ensembl ID: ENSGGOG00000002948
• Aliases: None
• Description: None

Sequence

>retro_ggor_1799
TTGACTTCAGAATTTGTAAACCCTGACATGGTACCTTTTGTTTTGCCCAGTGTTCTACTGATCGTTGAGGAATGCACCAA
AGAAGAATATGTCACATTAATTCCACCTGAACTTGGCCCTGTGTTTAAGCAGCAGGAGCCAATCCAGATTTTGTTAATTT
TCCTGCAAAAAATGGATTTGCTACTAACCAAAACCCCTCCCAATGAGATAAAGAACAGTGTTCTACCCATGGTTTACAGA
GCACTAGAAGCTCCTTCCATTCAATACCAGGAGCTCTGTCTAAACATCATTCCAACCTTTGCAAATCTTATAGACTACCC
ATCATGAGACATACTTTGATACCAAGAATTAAAAATGCCTGTCTACAAATGTCTTCCCTTGCTGTTCCTGTAAATTCATT
AGTGTGCTTAGGAAAGATTTTGGAATACTTGGATAAGTGGTTTTTACTTGATGATATCCTACCCTTCTTACAACAGATTC
CATCCAAAGAGTCTGCAGTCCTCATGGGTATTTTAGGCATTTACAAATGTACTTTTACTCATAAGTTGGGAATCACCAAA
GAGCAGCTGACTGGAAAAGTATTGCCTCATCTTATTCCCCTGAGTATTGAAAACAATCTTAATCAGTTCAATTCTTTCAT
TTCCGTCATAAAAGAGATGCTGAATAGGTTGGAGTCTGAACATAAGACTAAGCTGGAGCAACTTCATATAATGCAAGAAC
AACAGAAATCTTTGGACATAGGAAATCAAATGAATGTTTCTGAGGAGACAAAAGTTACAAATATTGGGAATCAGCAAATT
GACAAGGTTTTTAGCCACATTGGAGCAGACCTTCTGACTGGCAGTGATTCCGAAAATAAAGAGGATGGGTTTCAGAATAA
ACATAAAAGAGCATCACTTACACTTGAAGAAAAACAAAAATTAGCAAGAGAACAAGAGCAGGCGTAGAAGTTGAAAGGCC
AGCAGCCTCTTAAACCCCAAGTGTACACAACTATTGCTGCTGTTAAACAGACTAAGGACTTGACAGACACATTGATGGAT
AATATGTCATCTTTGACTAGCCTTTCTGTTAGTACCCCTAAACCTTCTGCTTCAAGTACGTTCACTTCTGTTCCTTCCAT
GGGCATTGGCATGATGTTTTCTACACCAGTTGATAATACAAAGAGAAATTTGACAAATGGCCTAAATGTCAATATGGGCT
TTCAGACTTCAGGATTCAACATGCCCGTTACTATAAACCAGAACTTCTACAGTAGTCCAAGCACAGTTGGAGTGACCAAA
ATGACTCTGGAACACCTCCCACTTTGCCAAACTTCAGTGCTTTGAATGTTCCTCCTGCTGGTGTGAAGCCAACCCAACAA
AGACCCACAGATATGTCTGCCCTTAATAATCTCTTTGGCCCTCAGAAACCCAAAGTTAGCATGAACCAATTATCACAACA
GAAACCAAATCAGTGGCTTAATCAGTTTGTACCTCCTCAAGTTTCTCCAGCTACGGGCAGTTCAGTAATGGGAACACAGA
TGAACATGATAGGACAATCTGCCTTTGGT

Alignment

ORF - retro_ggor_1799 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.95 %
• Parental protein coverage: 55.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LTSEFVNPDMVPFVLPNVLLIAEECTKEEYVKLILPELGPVFKQQEPIQILLIFLQKMDLLLTKTPPDEI
          LTSEFVNPDMVPFVLP.VLLI.EECTKEEYV.LI.PELGPVFKQQEPIQILLIFLQKMDLLLTKTPP.EI
Retrocopy LTSEFVNPDMVPFVLPSVLLIVEECTKEEYVTLIPPELGPVFKQQEPIQILLIFLQKMDLLLTKTPPNEI

Parental  KNSVLPMVYRALEAPSIQIQELCLNIIPTFANLIDYPS-MKNALIPRIKNACLQTSSLAVRVNSLVCLGK
          KNSVLPMVYRALEAPSIQ.QELCLNIIPTFANLIDYPS.M...LIPRIKNACLQ.SSLAV.VNSLVCLGK
Retrocopy KNSVLPMVYRALEAPSIQYQELCLNIIPTFANLIDYPS<MRHTLIPRIKNACLQMSSLAVPVNSLVCLGK

Parental  ILEYLDKWFVLDDILPFLQQIPSKEPAVLMGILGIYKCTFTHKKLGITKEQLAGKVLPHLIPLSIENNLN
          ILEYLDKWF.LDDILPFLQQIPSKE.AVLMGILGIYKCTFTHK.LGITKEQL.GKVLPHLIPLSIEN..N
Retrocopy ILEYLDKWFLLDDILPFLQQIPSKESAVLMGILGIYKCTFTHK-LGITKEQLTGKVLPHLIPLSIEN--N

Parental  LNQFNSFISVIKEMLNRLESEHKTKLEQLHIMQEQQKSLDIGNQMNVSEETKVTNIGNQQIDKVFNNIGA
          LNQFNSFISVIKEMLNRLESEHKTKLEQLHIMQEQQKSLDIGNQMNVSEETKVTNIGNQQIDKVF..IGA
Retrocopy LNQFNSFISVIKEMLNRLESEHKTKLEQLHIMQEQQKSLDIGNQMNVSEETKVTNIGNQQIDKVFSHIGA

Parental  DLLTGSESENKEDGLQNKHKRASLTLEEKQKLAKEQEQAQKLKSQQPLKPQVHTPIATVKQTKDLTDTLM
          DLLTGS.SENKEDG.QNKHKRASLTLEEKQKLA.EQEQA.KLK.QQPLKPQV.T.IA.VKQTKDLTDTLM
Retrocopy DLLTGSDSENKEDGFQNKHKRASLTLEEKQKLAREQEQA*KLKGQQPLKPQVYTTIAAVKQTKDLTDTLM

Parental  DNMSSLTSLSVSTPKSSASSTFTSVPSMGIGMMFSTPTDNTKRNLTNGLNANMGFQTSGFNMPVNTNQNF
          DNMSSLTSLSVSTPK.SASSTFTSVPSMGIGMMFSTP.DNTKRNLTNGLN.NMGFQTSGFNMPV..NQNF
Retrocopy DNMSSLTSLSVSTPKPSASSTFTSVPSMGIGMMFSTPVDNTKRNLTNGLNVNMGFQTSGFNMPVTINQNF

Parental  YSSPSTVGVTKMTL-GTTPTLPNFNALSVPPAGAKQTQQRPTDMSALNNLFGPQKPKVSMNQLSQQKPNQ
          YSSPSTVGVTKMTL.GT.PTLPNF.AL.VPPAG.K.TQQRPTDMSALNNLFGPQKPKVSMNQLSQQKPNQ
Retrocopy YSSPSTVGVTKMTL<GTPPTLPNFSALNVPPAGVKPTQQRPTDMSALNNLFGPQKPKVSMNQLSQQKPNQ

Parental  WLNQFVPPQGSPAMGSSVMGTQMNVIGQSAFG
          WLNQFVPPQ.SPA.GSSVMGTQMN.IGQSAFG
Retrocopy WLNQFVPPQVSPATGSSVMGTQMNMIGQSAFG

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	0.10 RPM	17.74 RPM
SRP007412_cerebellum	0.08 RPM	14.22 RPM
SRP007412_heart	0.00 RPM	4.00 RPM
SRP007412_kidney	0.12 RPM	36.92 RPM
SRP007412_liver	0.11 RPM	21.34 RPM
SRP007412_testis	0.00 RPM	72.73 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1799 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1799 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,