RetrogeneDB ID: retro_ptro_2337

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:30815227..30816519(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUCLA2
• Ensembl ID: ENSPTRG00000005859
• Aliases: None
• Description: None

Sequence

>retro_ptro_2337
CGGACCACACTGCGGGCTGCTGCTCAGGTTCTGGGAAGTTCTGGATTGTTTAATAACCGTGGACTCCAAGTACAGCAGCA
ACAGCAAAGGAATCTCTCACTACATGAATACATGAGTATGGAATTATTGCAAGAAACTGGTGTCTCTGTTCCCAAAGGAT
ATGTGGCAAAGTGACCAGATGAAGCTTATGCAATTGCCAAAAAATTAGGTTCAAAAGATGTTGTGATGAAGGCACAGGTT
TTAGCTGGTGGTAGAGGAAAAGGAACATTTGAAAGTGGCCTCAAAGGAGGGGTGAAGATGGTTTTCTCTCCAGAAGAAGC
AAAAGCTGTTCCTTCACAAATGATTAGGAAACAGTTGTTTACCAAGCAAATGAGAGAAAAGGGCAGAATATGCAATCAGG
TATTGGTCTGTGAGTGAAAATATCCCAAGAGAGAGTGCTACTTTGCAAAAACAATGGAAAGGTCATTTCAAGGTCTTGTA
TTAATAGGAAGTTTACATAGTGGGGCCAACATTGAAGATGTTGCTGCTGAGACTCCTGAAGCAATAATTAAAGTACCTAT
TGATATTGTAGAAGGTATCAAAGAGGAATAAGCTCTCCAGCTTGCACAGAAGATGGGATTTCCATCTAATATTGTGGCTT
CAGCAGCAGAAAACATGATCAAGCTTTACAGCCTTTTTCTGAAATACGATGCAACCGTGATAGAAATAAATTCAATGGTG
GAAGATTCAGATGGAGCTGTATTGTGTATGGATGCAAAGATCAATTTTGACTCTAATTCAGCCTATCGCCAAAAGAAAAT
CTTTGATCTACAGGACTGGACCCAGGAAGATGAAAGGAACAAAGATGCTGCTAAGGCAGATCTCAACTACACTGGCCTCG
ATGGAAGTATAGGCTGCCTAGTAAATGGTGCTGGTTTGGCTATGGCCACAATGGATATAATAAAACTTCATGGAGAGACT
CCAGCTAACTTCCTTGATGCTGGTGGTGGTGCTACAGTCCATCAAGTAACAGAAGCATTTAAGCCTATCACTTCAGCTAA
AAAGGTACTGGCTATTCTAGTCAACATTTGTGGAGGAATCATGCACTGTGATATTACAGCAAAGGGTATAGTCACGGCAG
TAAAAGGTTTGGAAATTAAGATACCTGTTGTGGTACAGTTACAAGTACACAAGTTGATGATGTTAAGGCACTAAAAGCAG
ACAGTGGACTTAAAATACTTGCTTGTGATGATTTGGTGGAAGCTGCTAGAGTGCTTGTAAAGCTCTCTGAAATAGTGAAG
CGAAGCAAGCGC

Alignment

ORF - retro_ptro_2337 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.81 %
• Parental protein coverage: 93.09 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RTAQRAAAQVLGSSGLFNNHGLQVQQQQQRNLSLHEYMSMELLQEAGVSVPKGYVAKSPDEAYAIAKKLG
          RT..RAAAQVLGSSGLFNN.GLQVQQQQQRNLSLHEYMSMELLQE.GVSVPKGYVAK.PDEAYAIAKKLG
Retrocopy RTTLRAAAQVLGSSGLFNNRGLQVQQQQQRNLSLHEYMSMELLQETGVSVPKGYVAK*PDEAYAIAKKLG

Parental  SKDVVIKAQVLAGGRGKGTFESGLKGGVKIVFSPEEAKAVSSQMIGKKLFTKQTGEKGRICNQVLVCERK
          SKDVV.KAQVLAGGRGKGTFESGLKGGVK.VFSPEEAKAV.SQMI.K.LFTKQ..EKGRICNQVLVCE.K
Retrocopy SKDVVMKAQVLAGGRGKGTFESGLKGGVKMVFSPEEAKAVPSQMIRKQLFTKQMREKGRICNQVLVCE*K

Parental  YPRREYYFAITMERSFQGPVLIGSSHGGVNIEDVAAETPEAIIKEPIDIEEGIKKEQALQLAQKMGFPPN
          YP.RE.YFA.TMERSFQG.VLIGS.H.G.NIEDVAAETPEAIIK.PIDI.EGIK.E.ALQLAQKMGFP.N
Retrocopy YPKRECYFAKTMERSFQGLVLIGSLHSGANIEDVAAETPEAIIKVPIDIVEGIKEE*ALQLAQKMGFPSN

Parental  IVESAAENMVKLYSLFLKYDATMIEINPMVEDSDGAVLCMDAKINFDSNSAYRQKKIFDLQDWTQEDERD
          IV.SAAENM.KLYSLFLKYDAT.IEIN.MVEDSDGAVLCMDAKINFDSNSAYRQKKIFDLQDWTQEDER.
Retrocopy IVASAAENMIKLYSLFLKYDATVIEINSMVEDSDGAVLCMDAKINFDSNSAYRQKKIFDLQDWTQEDERN

Parental  KDAAKANLNYIGLDGNIGCLVNGAGLAMATMDIIKLHGGTPANFLDVGGGATVHQVTEAFKLITSDKKVL
          KDAAKA.LNY.GLDG.IGCLVNGAGLAMATMDIIKLHG.TPANFLD.GGGATVHQVTEAFK.ITS.KKVL
Retrocopy KDAAKADLNYTGLDGSIGCLVNGAGLAMATMDIIKLHGETPANFLDAGGGATVHQVTEAFKPITSAKKVL

Parental  AILVNIFGGIMRCDVIAQGIVMAVKDLEIKIPVVVRLQ-GTRVDDAKALIADSGLKILACDDLDEAARMV
          AILVNI.GGIM.CD..A.GIV.AVK.LEIKIPVVV.LQ..T.VDD.KAL.ADSGLKILACDDL.EAAR..
Retrocopy AILVNICGGIMHCDITAKGIVTAVKGLEIKIPVVVQLQ<STQVDDVKALKADSGLKILACDDLVEAARVL

Parental  VKLSEIVTLAKQ
          VKLSEIV...K.
Retrocopy VKLSEIVKRSKR

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	0.23 RPM	52.16 RPM
SRP007412_cerebellum	0.14 RPM	40.80 RPM
SRP007412_heart	0.12 RPM	90.79 RPM
SRP007412_kidney	0.08 RPM	56.54 RPM
SRP007412_liver	0.00 RPM	8.67 RPM
SRP007412_testis	0.00 RPM	19.81 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2337 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2337 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2337 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3445
Gorilla gorilla	retro_ggor_2327
Pongo abelii	retro_pabe_2852

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 22 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,
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 ,