RetrogeneDB ID: retro_ggor_2327

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:31404594..31405887(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUCLA2
• Ensembl ID: ENSGGOG00000008224
• Aliases: None
• Description: None

Sequence

>retro_ggor_2327
CGGACCACACTGCGTGCTGCTGCTCAGGTTCTGGGAAGTTCTGGATTGTTTAATAACCATGGACTCCAAGTACAGCAGCA
ACAGCAAAGGAATCTCTCACTACATGAATACATGAGTATGGAATTATTACAAGAAACTGGTGTCTCTGTTCCCAAAGGAT
ATGTGGCAAAGTGACCAGATGAAGCTTATGCAATTGCCAAAAAATTAGGTTCAAAAGATGTTGTGATGAAGGCACAGGTT
TTAGCTGGTGGTAGAGGAAAAGGAACATTTGAAAGTGGCCCCAAAGGAGGGGTGAAGATGGTTTTCTCTCCAGAAGAAGC
AAAAGCTGTTCCTTCACAAATGATTAGGAAACAGTTGTTTACCAAGCAAATGGGAGAAAAGGGCAGAATATGCAATCAGG
TGTTGGTCTGTGAGTGAAAATATCCCAAGAGAGAGTGCTACTTTGCAATAACAATGGAAAGGTCATTTCAAGGTCTTGTA
TTAATAGGAAGTTTACATAGTGGGGCCAACATTGAAGATGTTGCTGCTGAGACTCCTGAAGCAATAATTAAAGTACCTAT
TGATATTGTAGAAGGTATCAAAGAGGAATAAGCTCTCCAGCTTGCACAGAAGTTGGGATTTCCATCTAATATTGTGGCTT
CAGCAGCAGAAAACATGATCAAGCTTTACAGCCTTTTTCTGAAATACGATGCAGCCGTGATAGAAATAAATTCAATGGTG
GAAGATTCAGATGGAGCTGTATTGTGTATGGATGCAAAGATCAGTTTTGACTCTAATTCAGCCTATCACCAAAAGAAAAT
CTTTGATCTACAGGACTGGACCCAGGAAGATGAAAGGAACAAAGAGGCTGCTAAGGCAGATCTCAACTACACTGGCCTCG
ATGGAAGTATAGGCTGCCTAGTAAATGGTGCTGGTTTGGCTATGGCCACAATGGATATAATAAAACATCATAGAAAGACT
CCAGCTAACTTCCTTGATGTTGGTGGTAGTGCTACAGTCCATCAAGTAACAGAAGCATTTAAGCCTATCACTTCAGATAA
AAAGGTACTGGCTATTCTGGTCAACGTTTGTGGAGGAATCATGCACTGTGATATTACAGCAAAGGGTATAGTCATGGCAG
TAAAAGGTTTGGAAATTAAAATACCTGTTGTGGTACAGTTACAAGGTACACAAGTTGATGATGTTAAGGCACTAAAAGCA
GACAGTGGACTTAAAATACTTGCTTGTGATGATTTGGTGGAAGCTGCTAGAGTGCTTGTAAAGCTCTCTGAAATAGTGAA
GCAAAGCAAGCGC

Alignment

ORF - retro_ggor_2327 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.31 %
• Parental protein coverage: 91.31 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RTAQRAAAQVLGSSGLFNNHGLQVQQQQQRNLSLHEYMSMELLQEAGVSVPKGYVAKSPDEAYAIAKKLG
          RT..RAAAQVLGSSGLFNNHGLQVQQQQQRNLSLHEYMSMELLQE.GVSVPKGYVAK.PDEAYAIAKKLG
Retrocopy RTTLRAAAQVLGSSGLFNNHGLQVQQQQQRNLSLHEYMSMELLQETGVSVPKGYVAK*PDEAYAIAKKLG

Parental  SKDVVIKAQVLAGGRGKGTFESGLKGGVKIVFSPEEAKAVSSQMIGKKLFTKQTGEKGRICNQVLVCERK
          SKDVV.KAQVLAGGRGKGTFESG.KGGVK.VFSPEEAKAV.SQMI.K.LFTKQ.GEKGRICNQVLVCE.K
Retrocopy SKDVVMKAQVLAGGRGKGTFESGPKGGVKMVFSPEEAKAVPSQMIRKQLFTKQMGEKGRICNQVLVCE*K

Parental  YPRREYYFAITMERSFQGPVLIGSSHGGVNIEDVAAETPEAIIKEPIDIEEGIKKEQALQLAQKMGFPPN
          YP.RE.YFAITMERSFQG.VLIGS.H.G.NIEDVAAETPEAIIK.PIDI.EGIK.E.ALQLAQK.GFP.N
Retrocopy YPKRECYFAITMERSFQGLVLIGSLHSGANIEDVAAETPEAIIKVPIDIVEGIKEE*ALQLAQKLGFPSN

Parental  IVESAAENMVKLYSLFLKYDATMIEINPMVEDSDGAVLCMDAKINFDSNSAYRQKKIFDLQDWTQEDERD
          IV.SAAENM.KLYSLFLKYDA..IEIN.MVEDSDGAVLCMDAKI.FDSNSAY.QKKIFDLQDWTQEDER.
Retrocopy IVASAAENMIKLYSLFLKYDAAVIEINSMVEDSDGAVLCMDAKISFDSNSAYHQKKIFDLQDWTQEDERN

Parental  KDAAKANLNYIGLDGNIGCLVNGAGLAMATMDIIKLHGGTPANFLDVGGGATVHQVTEAFKLITSDKKVL
          K.AAKA.LNY.GLDG.IGCLVNGAGLAMATMDIIK.H..TPANFLDVGG.ATVHQVTEAFK.ITSDKKVL
Retrocopy KEAAKADLNYTGLDGSIGCLVNGAGLAMATMDIIKHHRKTPANFLDVGGSATVHQVTEAFKPITSDKKVL

Parental  AILVNIFGGIMRCDVIAQGIVMAVKDLEIKIPVVVRLQGTRVDDAKALIADSGLKILACDDLDEAARMVV
          AILVN..GGIM.CD..A.GIVMAVK.LEIKIPVVV.LQGT.VDD.KAL.ADSGLKILACDDL.EAAR..V
Retrocopy AILVNVCGGIMHCDITAKGIVMAVKGLEIKIPVVVQLQGTQVDDVKALKADSGLKILACDDLVEAARVLV

Parental  KLSEIVTLAKQ
          KLSEIV...K.
Retrocopy KLSEIVKQSKR

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	0.05 RPM	66.85 RPM
SRP007412_cerebellum	0.04 RPM	36.21 RPM
SRP007412_heart	0.00 RPM	17.48 RPM
SRP007412_kidney	0.08 RPM	45.22 RPM
SRP007412_liver	0.03 RPM	11.47 RPM
SRP007412_testis	0.00 RPM	37.81 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_2327 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2327 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3445
Pan troglodytes	retro_ptro_2337
Pongo abelii	retro_pabe_2852

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014610	2 retrocopies	retro_acar_26, retro_acar_52,
Callithrix jacchus	ENSCJAG00000009278	2 retrocopies	retro_cjac_1233, retro_cjac_2379,
Cavia porcellus	ENSCPOG00000014961	1 retrocopy	retro_cpor_1113,
Homo sapiens	ENSG00000136143	3 retrocopies	retro_hsap_2236, retro_hsap_2281, retro_hsap_3445,
Gorilla gorilla	ENSGGOG00000008224	3 retrocopies	retro_ggor_1668, retro_ggor_1694, retro_ggor_2327 ,
Gorilla gorilla	ENSGGOG00000027438	1 retrocopy	retro_ggor_825,
Macaca mulatta	ENSMMUG00000007539	1 retrocopy	retro_mmul_1231,
Mustela putorius furo	ENSMPUG00000001488	1 retrocopy	retro_mputfur_768,
Nomascus leucogenys	ENSNLEG00000002948	3 retrocopies	retro_nleu_1963, retro_nleu_2140, retro_nleu_2302,
Otolemur garnettii	ENSOGAG00000007452	1 retrocopy	retro_ogar_2196,
Pongo abelii	ENSPPYG00000005352	2 retrocopies	retro_pabe_1939, retro_pabe_2852,
Pan troglodytes	ENSPTRG00000005859	3 retrocopies	retro_ptro_1581, retro_ptro_1615, retro_ptro_2337,