RetrogeneDB ID: retro_mdom_1324

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:13532692..13534276(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000021055
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC5A1
• Ensembl ID: ENSMODG00000009915
• Aliases: None
• Description: solute carrier family 5 (sodium/glucose cotransporter), member 1 [Source:HGNC Symbol;Acc:11036]

Sequence

>retro_mdom_1324
GCAGACATTGCCATTGTGGCCCTGTACTTTGTGCTGGTCATGTGCATTGGCTTCTTTGCCATGTGGAAGTCCAATAGGAG
CACCGTGAGTGGATACTTCCTGGCGGGGCGCTCTATGACCTGGGTAGCTATCGGGGCCTCTTTGTTTGTGAGCAATATTG
GCAGCGAGCACTTCATTGGGCTGGCGGGATCCGGAGCCGCCAGCGGATTCGCGGTGGGTGCGTGGGAGTTCAACGCCTTA
ATGCTTTTGCAGCTTCTCGGATGGGTTTTCATCCCCGTCTACATCCGCTCGGGCGTGTACACCATGCCCGAGTACTTGTC
CAAGCGCTTCGGCGGCCACAGGATTCAGGTCTATTTTGCAGCCTTGTCTTTACTGCTCTATATTTTCACCAAGCTTTCCG
TCGATCTGTACTCAGGGGCCCTCTTCATCCAGGAGTCTTTGGGCTGGAACCTCTACGTGTCTGTGATCCTGCTCATCGCC
ATGACGGCTCTGCTCACGGTCACGGGCGGCCTCGTGGCCGTCATCTACACGGACACCCTTCAGGCTTTGCTCATGATCGT
GGGGGCGCTGACGCTCATGGTCATCAGCATGATGAAGGTGGGCGGCTTCGAGGAGGTGAAGAAAAGGTACATGTTGGCCA
AGCCCAACGAGACCTCCATTCTGTTGACCTACAACCTGTCCAACACCAATTCTTGTCACGTCCACCCCAAGCCGGACGCG
CTCAAGATGCTGCGCGAGCCCACGGACGAAGACGTCCCCTGGCCCGGGTTCATCCTGGGCCAGACTCCGGCGTCCGTGTG
GTACTGGTGTGCTGACCAGGTGATCGTGCAGAGGGTCTTGGCCGCCAAGAACATCGCCCATGCCAAGGGCTCCACGCTCA
TGGCCGGCTTCTTGAAGCTTCTGCCCATGTTCATCATCGTGGTGCCGGGCATGATCTCCAGGATACTCTTTGCCGACGAT
CTTGCCTGCATCAACCCGGAGCACTGCATGCGAGTGTGTGGGAGCCGGGCCGGATGCTCCAACATCGCCTATCCGCGCCT
GGTCATGAATCTGGTCCCCGTGGGCCTCCGAGGACTGATGATGGCTGTCATGATCGCCGCGCTGATGAGTGATCTGGACT
CCATCTTCAACAGCGCCAGCACCATCTTCACGCTGGACGTGTACAAGCTCATTCGCAAAACGGCGAGCTCAAGAGAGCTC
ATGATCGTGGGGAGAGTTTTTGTGGCCTTCATGGTCGTGATCAGCATCGCGTGGGTGCCCATCATCGTGGAGATGCAAGG
GGGCCAGATGTACCTCTACATTCAGGAGGTGGCCGATTATCTGACGCCCCCCGTGGCTGCCCTCTTCCTTTTGGCCATCT
TCTGGAAGCGCTGCAATGAACAAGGGGCGTTTTATGGTGGAATGGCCGGCTTTATTTTAGGGGCGCTTCGCTTGATCCTG
GCCTTTACCTACCGCGCCCCAGAATGCGACCAGCCCGACGAGAGGCCAGCCTTCATAAAAAACATCCATTACATGTACGT
GGCCACCGCTTTGTTTTGGATCACAGGACTCATCACCGTGGTAGTGAGCCTCCTCACACCGCCC

Alignment

ORF - retro_mdom_1324 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.73 %
• Parental protein coverage: 79.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ADILVIILYFVVVLAVGLWAMFSTNRGTVGGFFLAGRSMVWWPIGASLFASNIGSGHFVGLAGTGAAAGI
          ADI....LYFV.V...G..AM...NR.TV.G.FLAGRSM.W..IGASLF.SNIGS.HF.GLAG.GAA.G.
Retrocopy ADIAIVALYFVLVMCIGFFAMWKSNRSTVSGYFLAGRSMTWVAIGASLFVSNIGSEHFIGLAGSGAASGF

Parental  ATGGFEWNALVLVVVLGWVFVPIYIKAGVVTMPEYLRKRFGGKRIQIYLSVLSLLLYIFTKISADIFSGA
          A.G..E.NAL.L...LGWVF.P.YI..GV.TMPEYL.KRFGG.RIQ.Y...LSLLLYIFTK.S.D..SGA
Retrocopy AVGAWEFNALMLLQLLGWVFIPVYIRSGVYTMPEYLSKRFGGHRIQVYFAALSLLLYIFTKLSVDLYSGA

Parental  IFINLALGLDLYLAIFLLLAITGLYTITGGLAAVIYTDTLQTAIMLVGSLILTGFAFNEVGGYEAFMDKY
          .FI...LG..LY....LL.A.T.L.T.TGGL.AVIYTDTLQ...M.VG.L.L.......VGG.E.....Y
Retrocopy LFIQESLGWNLYVSVILLIAMTALLTVTGGLVAVIYTDTLQALLMIVGALTLMVISMMKVGGFEEVKKRY

Parental  MKSIP---SKISEGNFTAKPECYT-PRADSFHLFRDPITGDLPWPGLIFGLGILALWYWCTDQVIVQRCL
          M...P...S.....N......C...P..D.....R.P...D.PWPG.I.G......WYWC.DQVIVQR.L
Retrocopy MLAKPNETSILLTYNLSNTNSCHVHPKPDALKMLREPTDEDVPWPGFILGQTPASVWYWCADQVIVQRVL

Parental  SAKNMSHVKAGCIMCGYLKLLPMFLMVMPGMISRILYTDKVACAVPSECEAQCGTKVGCSNIAYPTLVVE
          .AKN..H.K....M.G.LKLLPMF..V.PGMISRIL..D..AC..P..C...CG...GCSNIAYP.LV..
Retrocopy AAKNIAHAKGSTLMAGFLKLLPMFIIVVPGMISRILFADDLACINPEHCMRVCGSRAGCSNIAYPRLVMN

Parental  LMPNGLRGLMLSVMLASLMSSLTSIFNSASTLFTMDIYTKCRKKASEKELMIAGRVFILVLIGISIAWVP
          L.P.GLRGLM..VM.A.LMS.L.SIFNSAST.FT.D.Y...RK.AS..ELMI.GRVF......ISIAWVP
Retrocopy LVPVGLRGLMMAVMIAALMSDLDSIFNSASTIFTLDVYKLIRKTASSRELMIVGRVFVAFMVVISIAWVP

Parental  IVQSAQSGQLFDYIQSITSYLGPPIAAVFLLAIFCKRVNEPGAFWGLIFGLLIGLSRMIAEFAYGTGSCM
          I....Q.GQ...YIQ....YL.PP.AA.FLLAIF.KR.NE.GAF.G...G...G..R.I..F.Y....C.
Retrocopy IIVEMQGGQMYLYIQEVADYLTPPVAALFLLAIFWKRCNEQGAFYGGMAGFILGALRLILAFTYRAPECD

Parental  EPSNCPKIICGVHYLYFAIILFAVSVITILIISLLTKP
          .P...P..I...HY.Y.A..LF..........SLLT.P
Retrocopy QPDERPAFIKNIHYMYVATALFWITGLITVVVSLLTPP

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	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1324 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1324 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica 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 14 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000007944	1 retrocopy	retro_apla_5,
Choloepus hoffmanni	ENSCHOG00000005940	1 retrocopy	retro_chof_2,
Callithrix jacchus	ENSCJAG00000011369	1 retrocopy	retro_cjac_2033,
Ficedula albicollis	ENSFALG00000007384	1 retrocopy	retro_falb_29,
Homo sapiens	ENSG00000100170	1 retrocopy	retro_hsap_105,
Gallus gallus	ENSGALG00000006728	1 retrocopy	retro_ggal_2,
Monodelphis domestica	ENSMODG00000009915	1 retrocopy	retro_mdom_1324 ,
Mustela putorius furo	ENSMPUG00000012749	1 retrocopy	retro_mputfur_837,
Oryctolagus cuniculus	ENSOCUG00000017569	1 retrocopy	retro_ocun_1633,
Otolemur garnettii	ENSOGAG00000003370	1 retrocopy	retro_ogar_2513,
Ochotona princeps	ENSOPRG00000010458	1 retrocopy	retro_opri_6,
Procavia capensis	ENSPCAG00000015157	1 retrocopy	retro_pcap_3,
Rattus norvegicus	ENSRNOG00000017775	1 retrocopy	retro_rnor_794,
Ictidomys tridecemlineatus	ENSSTOG00000006386	1 retrocopy	retro_itri_13,