RetrogeneDB ID: retro_acar_109

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 3:142681753..142683199(-)
• Located in intron of: ENSACAG00000005071

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC5A2
• Ensembl ID: ENSACAG00000011926
• Aliases: None
• Description: solute carrier family 5 (sodium/glucose cotransporter), member 2 [Source:HGNC Symbol;Acc:11037]

Sequence

>retro_acar_109
ACCATGCCTGGGTACTTATCCAAACGATTTGGAGGTCATAGAATTCAAGTATACTTTGCAGTACTGTCTCTAATACTTTA
CATCTTCACCAAACTTTCAGTAGACTTATATTCAGGTGCACTATTCATTCAAGAATCGCTGGGTTGGAATATTTATTTGT
CAGTTATTTTACTGATTGGAATGACTGCATTGTTGACAGTGACAGGAGGTCTTGTGGCAGTCATCTACACAGACACGGTC
CAAGCTTTGCTTATGATTATTGGTGCCTTCACCCTTATGATCATAAGTATTACAGAAGTTGGAGGGTTTGAAGAACTTAA
AAGAAGATACATGTTGGCAAAACCTAATGTTACATCTATCTTGTTGACATATAACCTCTCCAATACTAATTCCTGCCATG
TTGATCCAAAGCCTGATTCACTGAGAATGTTGCGTGAACCAACGGATGAAGATATACCTTGGCCTGGTTTCCTTTTGGGA
CAGACTCCAGCTTCTGTATGGTACTGGTGTGCAGACCAAGTCATTGTTCAGCGTGTTCTAGCAGCAAAAAATATTGCTCA
TGCTAAAGGATCTACTCTAATGGCAGGTTTTCTAAAGCTTTTACCAATGTTCCTTATAGTTGTTCCGGGAATGATTTCAC
GAATACTATTTCCAGAAGACATTGCGTGTATCAATCCGGAACACTGTATGCAAGTTTGTGGGAGCAGAGCAGGATGCTCT
AATATTGCCTATCCACGTTTGGTAATGAGACTCGTTCCTGTTGGCCTGCGAGGCCTTATGATGGCTGTTATGATTGCTGC
ACTGATGAGTGATCTGGATTCTATATTTAATAGTGCCAGTACCATATTCACCCTTGACATCTACAAACTCCTCATAAGGA
AGGGAGCGTCATCTAGAGAACTGATGATTGTTGGAAGGGTTTTTGTTGCTTTCATGGTGGTAATAAGCATTGCTTGGGTC
CCAATAATAGTGGAAATGCAAGGAGGCCAAATGTATCTGTATATCCAAGAGGTAGCAGATTATTTGACACCACCAGTGGC
TGCTATATTTCTTATGGGTGTATTTTGGAAACGTTGCAATGAGCAAGGGGCCTTCTTTGGTGGAATGGTTGGTTTTGGTT
TGGGAGCTATTCGACTGATACTGGCATTTATATATCGTGTCCCGGAATGTAATCAACCAGACACTAGGCCACTCTTTATC
AAAAGTGTCCATTATATGTATTTTGCTACTGGGCTGTTCTGGATCACTGGAATTGTGGCTGTAATAGTCAGCTTTCTGAC
ACCACCACCATCAAAGGAGCAAATTCGGATGACAACATTCTGGTCTAGGAAAAGCAGGACAGTAAAAGAAAGCACTTCTG
TGGGCAATTCATTGACAGTACAAGAGAAAACCATTTTAAAATACAGTGAAACCTCCAATCCTGTATCTTCAAATGGAAAA
TCTGAA

Alignment

ORF - retro_acar_109 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.62 %
• Parental protein coverage: 70.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TMPQYLKKRFGGQRIRLYLSILSLFMYIFTKISVDMFSGAVFIQQALGWNIYVAVIALLIITTIYTVTGG
          TMP.YL.KRFGG.RI..Y...LSL..YIFTK.SVD..SGA.FIQ..LGWNIY..VI.L...T...TVTGG
Retrocopy TMPGYLSKRFGGHRIQVYFAVLSLILYIFTKLSVDLYSGALFIQESLGWNIYLSVILLIGMTALLTVTGG

Parental  LAALMYTDTVQTFVMVSGAFVLMGFAFNEVGGYQGVFDKYMEALPRQRLSPAPDLYNISA--SCY-QPRE
          L.A..YTDTVQ...M..GAF.LM.....EVGG.......YM..L...........YN.S...SC...P..
Retrocopy LVAVIYTDTVQALLMIIGAFTLMIISITEVGGFEELKRRYM--LAKPNVTSILLTYNLSNTNSCHVDPKP

Parental  DSFHMIRDAVTSDMPWPAVILGLTINSIWYWCSDQVIVQRCLAGKNLTHVKAGCILCGYLKLLPMFLMIM
          DS..M.R.....D.PWP...LG.T..S.WYWC.DQVIVQR.LA.KN..H.K......G.LKLLPMFL...
Retrocopy DSLRMLREPTDEDIPWPGFLLGQTPASVWYWCADQVIVQRVLAAKNIAHAKGSTLMAGFLKLLPMFLIVV

Parental  PGMISRILYPDDVACVIPEECMRICGTEVGCSNIAYPKLVVALMPNGLRGLMLAVMLAALMSSLASIFNS
          PGMISRIL.P.D.AC..PE.CM..CG...GCSNIAYP.LV..L.P.GLRGLM.AVM.AALMS.L.SIFNS
Retrocopy PGMISRILFPEDIACINPEHCMQVCGSRAGCSNIAYPRLVMRLVPVGLRGLMMAVMIAALMSDLDSIFNS

Parental  SGTLFTMDIYNRL-RPQAHDKELLIVGRVWILVLVGISIAWIPIVQAAQGGQLFDYIQSVSSYLAPPIAA
          ..T.FT.DIY..L.R..A...EL.IVGRV.....V.ISIAW.PI....QGGQ...YIQ.V..YL.PP.AA
Retrocopy ASTIFTLDIYKLLIRKGASSRELMIVGRVFVAFMVVISIAWVPIIVEMQGGQMYLYIQEVADYLTPPVAA

Parental  IFLLGVFIKRVNEQGAFWGLVAGLAIGMARMIPEFIYGTGSCLFPSSCPRLICGVHYLYFSVILFSATAV
          IFL.GVF.KR.NEQGAF.G...G...G..R.I..FIY....C..P...P..I..VHY.YF...LF..T..
Retrocopy IFLMGVFWKRCNEQGAFFGGMVGFGLGAIRLILAFIYRVPECNQPDTRPLFIKSVHYMYFATGLFWITGI

Parental  ITMVVSLCTPPIHDKHLHRLVFSLRYSKEERIDLDTEEEEEAKLKEAARQQQIEMAQAKNGKLE
          ....VS..TPP..........F..R.S.................K..............NGK.E
Retrocopy VAVIVSFLTPPPSKEQIRMTTFWSRKSRTVKESTSVGNSLTVQEKTILKYSETSNPVSSNGKSE

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	1.54 RPM	13.92 RPM
SRP009831_brain	7.20 RPM	7.48 RPM
SRP009831_dewlap	2.74 RPM	0.59 RPM
SRP009831_embryo	16.80 RPM	14.05 RPM
SRP009831_heart	1.35 RPM	3.06 RPM
SRP009831_liver	0.49 RPM	10.63 RPM
SRP009831_lung	7.10 RPM	6.30 RPM
SRP009831_ovary	2.39 RPM	0.15 RPM
SRP009831_skeletal_muscle	0.07 RPM	1.75 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_109 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_109 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011926	1 retrocopy	retro_acar_109 ,
Ailuropoda melanoleuca	ENSAMEG00000016218	1 retrocopy	retro_amel_32,
Bos taurus	ENSBTAG00000010096	1 retrocopy	retro_btau_287,
Canis familiaris	ENSCAFG00000016909	1 retrocopy	retro_cfam_157,
Felis catus	ENSFCAG00000001380	1 retrocopy	retro_fcat_110,
Latimeria chalumnae	ENSLACG00000007334	1 retrocopy	retro_lcha_35,
Loxodonta africana	ENSLAFG00000005737	1 retrocopy	retro_lafr_54,
Myotis lucifugus	ENSMLUG00000011500	1 retrocopy	retro_mluc_218,
Mus musculus	ENSMUSG00000030781	1 retrocopy	retro_mmus_200,
Pteropus vampyrus	ENSPVAG00000012531	1 retrocopy	retro_pvam_13,
Tursiops truncatus	ENSTTRG00000012500	1 retrocopy	retro_ttru_2,