RetrogeneDB ID: retro_gacu_20

Retrocopy location

• Organism: Stickleback (Gasterosteus aculeatus)
• Coordinates: groupXII:809544..810582(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGACG00000002863
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSGACG00000001398
• Aliases: None
• Description: None

Sequence

>retro_gacu_20
AACGGCACAGAGGGACCCTACTTCTACGTCCCCATGATGAACACCACGGGAATCGTGCGGAGTCCTTATGAATACCCTCA
GTACTACCTTGTCAACCCGGCGGCCTACGCCGCCCTGGGGGCCTACATGTTCCTGCTCATCCTCGTGGGCTTCCCCGTCA
ACTTCCTCACCCTCTACGTCACCCTCGAACACAAGAAGCTGCGGACCCCTCTAAACTACATCCTGCTGAACCTGGCGGTG
GCCGACCTCTTCATGGTGCTGGGCGGGTTCACCACGACCATGTACACCTCCATGCACGGCTACTTCGTCCTGGGTCGCCT
GGGCTGCAACGTGGAGGGCTTCTGCGCCACGCTGGGCGGCGAGATCGCCCTGTGGTCGCTGGTGGTCCTGGCCGTGGAAA
GGTGGGTGGTCGTCTGCAAGCCCATCGCCAACTTCCGCTTCGGCGAGGACCACGCCATCATGGGTCTGGCCCTCACCTGG
GTCATGGCCGCGGCCTGCGCCGTGCCGCCCCTGGTCGGCTGGTCCCGCTACATCCCCGAGGGCATGCAGTGCTCGTGCGG
AGTCGACTACTACACGCGTGCCCGAGGGTTCAGACAACGGAAGCGTTCGTCATCTACATGTTCGGTCTGCCACTTACATG
ATCCCGATGATGATCATTTTCTTCTGCTACGGACGGCTGCTGTGCGCCGTCAAGGGAGGCCGCCGCCGCCCAGCAGGAGT
CCGAGACCACCCAAAAGGCCGAGAGGGGAGGTCAGCCGCATGGTGGTGATCATGGTCATCGCCTTCCTGGTGTGCTGGGT
GCCCTACGCCAGCGTGGCCTGGTTTATCTTCTGCAATCAGGGATCCGAGTTCGGACCCGTCTTCATGACCATCCCGGCCT
TCTTTGCCAAGAGCTCGTCCGTCTACAACCCGTTGATCTACATCTGCATGAACAAGCAGTTCCGCCACTGCATGATCACC
ACATTGTGCTGCGGGAAGAATCCCTTCGAGGAGGAGGAGGGAGCGTCCTCCACGAAGACCGAGGCCTCCTCCGTCTCC

Alignment

ORF - retro_gacu_20 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.14 %
• Parental protein coverage: 97.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  NGTEGKNFYIPMSNRTGVVRSPFEYQQYYLADPIMFKILALYMFFLICTGTPINGLTLLVTAQNKKLRQP
          NGTEG..FY.PM.N.TG.VRSP.EY.QYYL..P.....L..YMF.LI..G.P.N.LTL.VT...KKLR.P
Retrocopy NGTEGPYFYVPMMNTTGIVRSPYEYPQYYLVNPAAYAALGAYMFLLILVGFPVNFLTLYVTLEHKKLRTP

Parental  LNYILVNLAVAGLIMCAFGFTITITSAVNGYFILGATACAVEGFMATLGGEVALWSLVVLAVERYIVVCK
          LNYIL.NLAVA.L.M...GFT.T......GYF.LG...C.VEGF.ATLGGE.ALWSLVVLAVER..VVCK
Retrocopy LNYILLNLAVADLFMVLGGFTTTMYTSMHGYFVLGRLGCNVEGFCATLGGEIALWSLVVLAVERWVVVCK

Parental  PMGSFKFSGTHAGAGVLFTWIMAMACAAPPLFGWSRYLPEGMQCSCGPDYYTLA-PGFNN-ESYVIYMF-
          P...F.F...HA..G...TW.MA.ACA.PPL.GWSRY.PEGMQCSCG.DYYT.A..G..N.E..VIYMF.
Retrocopy PIANFRFGEDHAIMGLALTWVMAAACAVPPLVGWSRYIPEGMQCSCGVDYYTRA>EGSDN>EAFVIYMF>

Parental  VVH-FFTPVFIIFFTYGSLVLTVKA-AAAQQQESESTQKAER-EVTRMCILMVFGFLVAWVPYASFAGWI
          V.H....P..IIFF.YG.L...VK..AAA.QQESE.TQKAER.EV.RM...MV..FLV.WVPYAS.A..I
Retrocopy VCH>YMIPMMIIFFCYGRLLCAVKG>AAAAQQESETTQKAER>EVSRMVVIMVIAFLVCWVPYASVAWFI

Parental  FLNKGAPFSALTAAIPAFFAKSSALYNPVIYVLLNKQFRNCMLTTIGMG-GMVEDETSVSASKTEVSSVS
          F.N.G..F......IPAFFAKSS..YNP.IY...NKQFR.CM.TT...G....E.E...S..KTE.SSVS
Retrocopy FCNQGSEFGPVFMTIPAFFAKSSSVYNPLIYICMNKQFRHCMITTLCCGKNPFEEEEGASSTKTEASSVS

Legend:

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

Expression

RNA-Seq

Gasterosteus aculeatus was not studied using RNA-Seq expression data.

ChIP-Seq

Gasterosteus aculeatus was not studied using ChIP-Seq data.

EST

Gasterosteus aculeatus was not studied using EST data.

TSS

Gasterosteus aculeatus was not studied using FANTOM5 data.

Lab

retro_gacu_20 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_gacu_20 has 1 orthologous retrocopies within teleost group .

Species	RetrogeneDB ID
Oryzias latipes	retro_olat_6

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Gasterosteus aculeatus	ENSGACG00000001398	1 retrocopy	retro_gacu_20 ,