RetrogeneDB ID: retro_acar_52

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343907.1:39114..40443(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000003836
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SUCLA2
• Ensembl ID: ENSACAG00000014610
• Aliases: None
• Description: succinate-CoA ligase, ADP-forming, beta subunit [Source:HGNC Symbol;Acc:11448]

Sequence

>retro_acar_52
CAGAGGATCCTGAGCGCCACGGCCAAAGCTTTGGGGTCCAGCCGGGGATTCGTCACCACCTGCAGGCGTCCAGTGCTGCA
GCAGCAGCTGCGGGATCTGTCTCTCCATGAATATTTGAGCATGAAGCTCTTGAAGGAAGAGGGCATCCCTGTCCCTTATG
GTTTGTTGGCCAGAACTCCGGAGGAGGCTTACACAGTGGCCAGAAAGATCGGCACCGATGACCTGGTGGTCAAGGCCCAG
GTGTTGACCGGTGGCCGGCAGAACGGGGTCTTCGAAGGGGGCCTGAGAGGAGGGGTGCAGGTGGTCTGCTCCCCAGAAGA
AGCCAGGGAGGTGGCCTCCAGGATGATCGGGAAGCGGCTGTTCACCCAGCAGACAGGCAAAATGGGCCGCATATGCAACC
AGGTCCTCATCTGCGAGCGCAAGTACCTCAGGCGGGAGTACTACTTTGCCATCACCATGGAGCGGGCCTTCCAGGGCCCC
GTCCTCATCGGCAGCTCCCAAGGAGGGGTGCGCATTGAGGACGTGGCTGCCGAGAACCCCGGGGCCATCATCAAGCAGCC
GGTGGACATCATGGAAGGCATCACCGAGGAGCAGGCTGTGCAGCTTGCCCAGAAGATGGGCTTTCCGCACCACTTGCTGT
ACGAGGTGGCCGACAACATGATTAAGATCTACAACTTCTTCATCAAATACGATGTCATCTTGCTCGAGATCAACCCGCTG
GTCGAAGACTCAACAGGGCATGTGATGTGCATGGACGCCAAGATTATTTTCGACAGCAACTCGGCCTTTCGCCAGCAGAA
GATCTTTGAGCTGCAGGACTGGACCCAGTTGGATGAGCGAGACCGGGAGGCGGCCAACGCGGAGCTGAACTACATTGCCT
TGGATGGCAACATCGGCTGCCTGGTCAATGGGGCTGGCCTGGCCATGGCCACCATGGACATCATCAAGCTCCACGGAGGC
ACCCCAGCCAACTACCTCAACGTTGGAGGCAGTGCCACAGTGGAGCAAGTCACGGAGGCCTTCAAGCTCATCACCTCCAA
CGAGAAAGTCCAGGCCATTCTGGTCAACATCTTTGGAGGGCTGATGAGGTGTGATGTCATTGCACATGGCATAATCATGT
CGGCCAAAGATCTGGACCTCAAAATCCCCATTGTGGTGCGGCTGCAAGGAACACGGGTCAAGGACGCAAAGAACTTGATT
GCTGAGAGCGGCCTGAAGATTCTTCCCTGCGATGACCTGGACCAAGCGGCCAAAATGGCCGTGAAGCTCTCTGAGATCAT
GGTCCTGGCCAAAGAGGCCCAGGTGGACGTCAAATTTCATTTGCCATGA

Alignment

ORF - retro_acar_52 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.89 %
• Parental protein coverage: 88.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLAAKILSGSPGLLSNHAFQI--EQRRNLSLHEYLSMELLKEAGISVPHGLVANTPEDAYNVAKQIGTKD
          S..AK.L..S.G............Q.R.LSLHEYLSM.LLKE.GI.VP.GL.A.TPE.AY.VA..IGT.D
Retrocopy SATAKALGSSRGFVTTCRRPVLQQQLRDLSLHEYLSMKLLKEEGIPVPYGLLARTPEEAYTVARKIGTDD

Parental  LVVKAQVLAGGRGKGTFEGGLKGGVKIVFSPEEAREISSRMIGKKLFTKQTGEKGRICNQVFICERRYPR
          LVVKAQVL.GGR..G.FEGGL.GGV..V.SPEEARE..SRMIGK.LFT.QTG..GRICNQV.ICER.Y.R
Retrocopy LVVKAQVLTGGRQNGVFEGGLRGGVQVVCSPEEAREVASRMIGKRLFTQQTGKMGRICNQVLICERKYLR

Parental  REYYFAITMERSFQGPVLIGSAQGGVNIEDVAAENPDAIAKEPVDIVEGIQKEQAIRLAKKMGFPANLVN
          REYYFAITMER.FQGPVLIGS.QGGV.IEDVAAENP.AI.K.PVDI.EGI..EQA..LA.KMGFP..L..
Retrocopy REYYFAITMERAFQGPVLIGSSQGGVRIEDVAAENPGAIIKQPVDIMEGITEEQAVQLAQKMGFPHHLLY

Parental  EAAENMIKIYNLFIKFDATMVEINPMVEDSTGIVMCMDAKINFDSNSAYRQQKIFSLQDWTQEDDRDRDA
          E.A.NMIKIYN.FIK.D....EINP.VEDSTG.VMCMDAKI.FDSNSA.RQQKIF.LQDWTQ.D.RDR.A
Retrocopy EVADNMIKIYNFFIKYDVILLEINPLVEDSTGHVMCMDAKIIFDSNSAFRQQKIFELQDWTQLDERDREA

Parental  AKSDLNYIGLDGSIGCLVNGAGLAMATMDIIKLHGGTPANFLDVGGGATAQRVTEAFRLITSDKKVQAIL
          A...LNYI.LDG.IGCLVNGAGLAMATMDIIKLHGGTPAN.L.VGG.AT...VTEAF.LITS..KVQAIL
Retrocopy ANAELNYIALDGNIGCLVNGAGLAMATMDIIKLHGGTPANYLNVGGSATVEQVTEAFKLITSNEKVQAIL

Parental  VNIFGGIMRCDVIAQGIIMAVKDLELKIPIVVRLQGTRVDDAKALITDSGLKILACDDLDEAAKMVVKLS
          VNIFGG.MRCDVIA.GIIM..KDL.LKIPIVVRLQGTRV.DAK.LI..SGLKIL.CDDLD.AAKM.VKLS
Retrocopy VNIFGGLMRCDVIAHGIIMSAKDLDLKIPIVVRLQGTRVKDAKNLIAESGLKILPCDDLDQAAKMAVKLS

Parental  EIVTLAKQAQVDVKFQLP
          EI..LAK.AQVDVKF.LP
Retrocopy EIMVLAKEAQVDVKFHLP

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
SRP009831_adrenal	0.62 RPM	84.75 RPM
SRP009831_brain	0.76 RPM	130.52 RPM
SRP009831_dewlap	0.00 RPM	27.59 RPM
SRP009831_embryo	0.59 RPM	98.07 RPM
SRP009831_heart	1.19 RPM	217.02 RPM
SRP009831_liver	0.08 RPM	55.10 RPM
SRP009831_lung	0.05 RPM	58.18 RPM
SRP009831_ovary	0.00 RPM	15.67 RPM
SRP009831_skeletal_muscle	0.00 RPM	127.44 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_52 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_52 was not experimentally validated.

Homology

Retrocopy orthology:

Anolis carolinensis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,