RetrogeneDB ID: retro_amel_32

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192682.1:263820..265974(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000019486
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SLC5A2
• Ensembl ID: ENSAMEG00000016218
• Aliases: None
• Description: None

Sequence

>retro_amel_32
ATGAGGGCTGTACTGGAGACAGCAGACATTGCCATAGTGGCCCTGTATTTTATCCTGGTCATGTGCATTGGTTTTTTTGC
AATGTGGAAATCTAATAGAAGCACCGTGAGTGGATACTTCCTGGCGGGGCGCTCTATGACCTGGGTAGCAATTGGTGCCT
CTCTGTTTGTGAGCAATATTGGGAGTGAGCACTTCATTGGGCTGGCAGGATCTGGAGCTGCAAGTGGATTTGCAGTGGGC
GCATGGGAATTCAATGCCTTACTGCTTTTGCAACTTCTGGGATGGGTTTTCATCCCTATTTACATCCGGTCAGGGGTATA
CACCATGCCTGAATACTTATCCAAGCGATTTGGTGGCCATAGGATTCAGGTCTATTTCGCAGCCTTGTCTCTGATTCTCT
ATATCTTCACCAAGCTCTCAGTGGATCTGTATTCGGGTGCCCTCTTTATCCAGGAGTCTTTGGGTTGGAACCTCTATGTG
TCTGTCATCCTGCTCATTGGCATGACTGCTTTGCTGACTGTCACCGGAGGCCTTGTTGCAGTGATCTACACAGACACTCT
GCAGGCTCTGCTTATGATCGTTGGGGCACTCACACTTATGATTATTAGCATGATGGAGATTGGCGGGTTTGAGGAAGTTA
AGAGAAGGTACATGTTGGCCTCACCCAATGTTACTTCCATCTTGTTGACATACAACCTTTCCAACACAAATTCTTGTAAT
GTTCACCCTAAGAAAGATGCACTGAAAATGTTGCGGAATCCAACAGATGAAGATGTTCCTTGGCCTGGATTCGTTCTTGG
GCAGACCCCAGCTTCAGTATGGTACTGGTGTGCTGACCAAGTCATCGTGCAGAGAGTCTTAGCAGCTAAAAACATTGCTC
ATGCCAAAGGCTCTACTCTTATGGCTGGCTTCTTGAAGCTTCTGCCAATGTTTATCATAGTTGTCCCAGGAATGATTTCC
AGGATACTGTTTGCTGATGATATAGCTTGCATCAACCCAGAGCACTGCATGCAAGTATGTGGAAGCAGAGCTGGGTGCTC
TAATATTGCTTACCCACGCCTGGTGATGAAGCTGGTTCCCGTGGGCCTCCGTGGCTTAATGATGGCAGTGATGATTGCAG
CTCTGATGAGCGACTTGGACTCTATCTTTAACAGTGCCAGTACCATATTCACCCTCGATGTGTACAAACTCATCCGCAGG
AGCGCAAGCTCCCGGGAACTAATGATTGTGGGGAGGATATTTGTGGCTTTTATGGTGGTGATCAGCATTGCATGGGTGCC
AATCATCGTGGAGATGCAAGGAGGCCAGATGTACCTTTATATTCAGGAGGTAGCAGATTACCTGACACCCCCAGTTGCGG
CCCTGTTCCTTCTGGCAATTTTCTGGAAGCGCTGCAATGAGCAAGGGGCTTTCTATGGTGGAATGGCTGGCTTTGTTCTT
GGAGCGGTCCGTTTGACACTGGCCTTTGCATACCGTGCCCCAGAATGTGACCAACCCGATAACAGGCCAGGCTTCATCAA
AGACATCCATTACATGTATGTGGCCACAGCATTGTTTTGGGTCACAGGACTCATTACTGTAATTGTTAGCCTTCTCACAC
CACCTCCCACAAAGGAACAGATTCGTACCACCACCTTTTGGTCTAAGAAGAGCCTGGTGGTGAAGGAAAGCTGCTCCCCG
AAAGATGAACCATACAAAATGCAAGAGAAGAGCATTCTGAGGTGCAGTGAGAACAGTGAGGCCATCAACCACATCATTCC
CAATGGGAAATCTGAAGATAGCATCAAGGGCCTTCAGCCGGAAGATGTTAATCTGTTGGTGACCTGCAGAGAAGAGGGCA
ATCCAGTGGCTTCATTAGGGCATTCAGAGGCAGAAACACCAGTAGATGCTTATTCCAATGGGCAAGCAGCTCTTATGGGT
GAGAAGGAGAGAAAGAAGGAAACAGAGGATGGAGGCCAGTACTGGAAGTTCATAGATTGGTTCTGTGGCTTTAAAAGTAA
GAGCCTCAGCAAGAGGAGTCTCAGAGACCTGATGGAGGAGGAGGCTGTCTGTTTACAAATGTTGGAAGAGCCTCCACAAG
TTAAACTAATACTGAATATCGGACTTTTTGCTGTGTGTTCACTTGGAATTTTCATGTTTGTTTATTTCTCCTTA

Alignment

ORF - retro_amel_32 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.09 %
• Parental protein coverage: 78.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ADILVIAAYFLLVIGVGLWSMCRTNRGTVGGYFLAGRSMVWWPVGASLFASNIGSGHFVGLAGTGAASGL
          ADI...A.YF.LV...G...M...NR.TV.GYFLAGRSM.W...GASLF.SNIGS.HF.GLAG.GAASG.
Retrocopy ADIAIVALYFILVMCIGFFAMWKSNRSTVSGYFLAGRSMTWVAIGASLFVSNIGSEHFIGLAGSGAASGF

Parental  AVAGFEWNALFVVLLLGWVFAPVYLTAGVITMPQYLRKRFGGHRIRLYLSMLSLFLYIFTKISVDMFSGA
          AV...E.NAL....LLGWVF.P.Y...GV.TMP.YL.KRFGGHRI..Y...LSL.LYIFTK.SVD..SGA
Retrocopy AVGAWEFNALLLLQLLGWVFIPIYIRSGVYTMPEYLSKRFGGHRIQVYFAALSLILYIFTKLSVDLYSGA

Parental  VFIQQALGWNIYASVIALLGITMIYTVTGGLAALMYTDTVQTFVILGGAFILMGYAFHEVGGYSGLFDKY
          .FIQ..LGWN.Y.SVI.L.G.T...TVTGGL.A..YTDT.Q......GA..LM.....E.GG.......Y
Retrocopy LFIQESLGWNLYVSVILLIGMTALLTVTGGLVAVIYTDTLQALLMIVGALTLMIISMMEIGGFEEVKRRY

Parental  LEAVTSLT-VSEDPEVGNISSSCYLPRPDSYHLLRDPVTGDLPWPALLLGLTIVSGWYWCSDQVIVQRCL
          ..A....T.........N..S....P..D....LR.P...D.PWP...LG.T..S.WYWC.DQVIVQR.L
Retrocopy MLASPNVTSILLTYNLSNTNSCNVHPKKDALKMLRNPTDEDVPWPGFVLGQTPASVWYWCADQVIVQRVL

Parental  AGKSLTHIKAGCILCGYLKLMPMFLMVMPGMISRILYPDEVACVVPEVCKRVCGTEVGCSNIAYPRLVVK
          A.K...H.K......G.LKL.PMF..V.PGMISRIL..D..AC..PE.C..VCG...GCSNIAYPRLV.K
Retrocopy AAKNIAHAKGSTLMAGFLKLLPMFIIVVPGMISRILFADDIACINPEHCMQVCGSRAGCSNIAYPRLVMK

Parental  LMPNGLRGLMLAVMLAALMSSLASIFNSSSTLFTMDIYTRLRPRAGDRELLLVGRLWVVLIVAVSVAWLP
          L.P.GLRGLM.AVM.AALMS.L.SIFNS.ST.FT.D.Y...R..A..REL..VGR..V...V..S.AW.P
Retrocopy LVPVGLRGLMMAVMIAALMSDLDSIFNSASTIFTLDVYKLIRRSASSRELMIVGRIFVAFMVVISIAWVP

Parental  VVQAAQGGQLFDYMQAVSSYLAPPVSAVFVLALFVPRVNEKGAFWGLIGGLLMGLARLIPEFSFGSGSCV
          .....QGGQ...Y.Q.V..YL.PPV.A.F.LA.F..R.NE.GAF.G...G...G..RL...F......C.
Retrocopy IIVEMQGGQMYLYIQEVADYLTPPVAALFLLAIFWKRCNEQGAFYGGMAGFVLGAVRLTLAFAYRAPECD

Parental  QPSACPALVCGMHYLYFAIVLFICSGLLTLVVSLCTAPIPRKHLHRLVFSLRHSKEERE
          QP...P......HY.Y.A..LF...GL.T..VSL.T.P..........F....S....E
Retrocopy QPDNRPGFIKDIHYMYVATALFWVTGLITVIVSLLTPPPTKEQIRTTTFWSKKSLVVKE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_32 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_32 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca 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.

---

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,