RetrogeneDB ID: retro_acar_26

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343907.1:42044..43424(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000003832
• 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_26
GAAGCAAGGCCCACCTCCTTCCATGAGCTGCAAGTGGGCTTCATGGGCCGGAGTGGGATCCTGGCAGCCTTTAATGCTGC
AGCCAAAGCATTTGGCGGGCGCTTGGGATCCTTCAGCCACGGTTTCCCCACACAACCACAAAGGAACCTGTCCCTGCACG
AATACCTGAGCATGAGGCTCCTGAAAGAAGCTGGTGTCTCTGTCCCAAATGGAGTGGTGGCCAGAACGCCAGGGGAGGCC
TTCAAAGCGGCCCAGAATATCGGTAGCAATGAGCTGGTGGTCAAGGCACAGGTGTTAGCTGGAGGTCGGGGGAAAGGGAC
CTTTGAAGGAGGCCTCAAGGGTGGAGTGAAGATTGTTTATTCCCCAGAAGAGGCTAAGGAAATGGCCTCCCAGATGATTG
GGAAGAAGCTGTTCACCAAACAGACGGGGGAAAGAGGCCGAATCTGCAACGAGGTCCTCATCTGCGAGCGCCGGTACCCC
AAGAAAGAGTACTACTTCGCCATTGCCCTGGAGCGGGCCTTCCAGGGCCCCGTGCTGATTGGCAGTGCCCAGGGGGGCGT
CAATATCGAAGACGTGGCTGCAGAGAACCCCGAGGCCATTGTCAAGGAGCCCGTGGACATCGTGGAGGGCATCCAGACAG
AGCAGGCCCTGCGCCTGGCCCAGAAAATGGGATTCCCTGCCGATGTGGCAGAAGATGCTGCCCATAACATGGTGAAGCTC
TACCAGTTCTTCATCAAATACGACGCCCTGATGGTGGAAATTAACCCCATGGTGGAGGACTCAACGGGGAAAGTGATCTG
CATAGACGCCAAGATCAACCTGGACAGCAACTCGGCCTTCCGGCAGAAGAGCGTCTTCGACCTGCAGGACTGGAGCCAGG
AGGACGAGCGGGACCGGGAGGCGGCCAACGCGCAGCTGAACTACGTTCCCTTGGATGGGGACATTGGCTGCCTGGTCAAT
GGGGCCGGCCTGGCCATGGCCACCATGGACATCATCAAGCTCCACGGAGGCACCCCGGCCAACTTCCTCGACGTGGGAGG
AGGGGCCTCCCCAGAGCAAGTCAAAGAGGCCTTCAAGCTCATCACGTCGGACACCAGGGTCCAGTCGGTCCTCGTGAACA
TCTTTGGGGGCATCATGCGATGCGACATCATTGCCCAAGGAATCATCATGGCTGCCTCGGAGCTGGACCTCAAAGTCCCC
ATCGTGGTGCGCTTGCAAGGAACACAAATGGAGAGCGCCAAGGCCTTGATCGCAAAGAGCGGCCTGAAGATCCTGCCCTG
CGACGACCTGGACCAGGCGGCCCAAATGGCCGTCAAGCTCTCCCAGATCATGACCCTGGCCCGGCAAGCCCGCCTGGACG
TCAAGTTCCAGCTGCAGAGC

Alignment

ORF - retro_acar_26 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.06 %
• Parental protein coverage: 87.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAKILSGSPGLLSNHAFQIEQRRNLSLHEYLSMELLKEAGISVPHGLVANTPEDAYNVAKQIGTKDLVVK
          AAK...G..G..S.H.F.....RNLSLHEYLSM.LLKEAG.SVP.G.VA.TP..A...A..IG...LVVK
Retrocopy AAKAFGGRLGSFS-HGFPTQPQRNLSLHEYLSMRLLKEAGVSVPNGVVARTPGEAFKAAQNIGSNELVVK

Parental  AQVLAGGRGKGTFEGGLKGGVKIVFSPEEAREISSRMIGKKLFTKQTGEKGRICNQVFICERRYPRREYY
          AQVLAGGRGKGTFEGGLKGGVKIV.SPEEA.E..S.MIGKKLFTKQTGE.GRICN.V.ICERRYP..EYY
Retrocopy AQVLAGGRGKGTFEGGLKGGVKIVYSPEEAKEMASQMIGKKLFTKQTGERGRICNEVLICERRYPKKEYY

Parental  FAITMERSFQGPVLIGSAQGGVNIEDVAAENPDAIAKEPVDIVEGIQKEQAIRLAKKMGFPANLVNEAAE
          FAI..ER.FQGPVLIGSAQGGVNIEDVAAENP.AI.KEPVDIVEGIQ.EQA.RLA.KMGFPA.....AA.
Retrocopy FAIALERAFQGPVLIGSAQGGVNIEDVAAENPEAIVKEPVDIVEGIQTEQALRLAQKMGFPADVAEDAAH

Parental  NMIKIYNLFIKFDATMVEINPMVEDSTGIVMCMDAKINFDSNSAYRQQKIFSLQDWTQEDDRDRDAAKSD
          NM.K.Y..FIK.DA.MVEINPMVEDSTG.V.C.DAKIN.DSNSA.RQ...F.LQDW.QED.RDR.AA...
Retrocopy NMVKLYQFFIKYDALMVEINPMVEDSTGKVICIDAKINLDSNSAFRQKSVFDLQDWSQEDERDREAANAQ

Parental  LNYIGLDGSIGCLVNGAGLAMATMDIIKLHGGTPANFLDVGGGATAQRVTEAFRLITSDKKVQAILVNIF
          LNY..LDG.IGCLVNGAGLAMATMDIIKLHGGTPANFLDVGGGA....V.EAF.LITSD..VQ..LVNIF
Retrocopy LNYVPLDGDIGCLVNGAGLAMATMDIIKLHGGTPANFLDVGGGASPEQVKEAFKLITSDTRVQSVLVNIF

Parental  GGIMRCDVIAQGIIMAVKDLELKIPIVVRLQGTRVDDAKALITDSGLKILACDDLDEAAKMVVKLSEIVT
          GGIMRCD.IAQGIIMA...L.LK.PIVVRLQGT....AKALI..SGLKIL.CDDLD.AA.M.VKLS.I.T
Retrocopy GGIMRCDIIAQGIIMAASELDLKVPIVVRLQGTQMESAKALIAKSGLKILPCDDLDQAAQMAVKLSQIMT

Parental  LAKQAQVDVKFQL
          LA.QA..DVKFQL
Retrocopy LARQARLDVKFQL

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	0.20 RPM	84.75 RPM
SRP009831_brain	0.43 RPM	130.52 RPM
SRP009831_dewlap	0.00 RPM	27.59 RPM
SRP009831_embryo	0.68 RPM	98.07 RPM
SRP009831_heart	0.00 RPM	217.02 RPM
SRP009831_liver	0.04 RPM	55.10 RPM
SRP009831_lung	0.30 RPM	58.18 RPM
SRP009831_ovary	0.00 RPM	15.67 RPM
SRP009831_skeletal_muscle	0.15 RPM	127.44 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_26 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_26 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,