RetrogeneDB ID: retro_meug_1229

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold33323:10994..12159(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PABPC1L
• Ensembl ID: ENSMEUG00000007905
• Aliases: None
• Description: poly(A) binding protein, cytoplasmic 1-like [Source:HGNC Symbol;Acc:15797]

Sequence

>retro_meug_1229
TTGAACACTGGGGCCACCAGTTACCCTGTGGCCTCCCTGTATGTGGTTGACCTGCACTCTGATATCCCAGAAGCCACGCT
GTACGAGAAGTTTAGCCTGGCCAGACTCATGCTCTTCGTCCAAGTCTGCAGGGACATGATCACCAGGCTCTCCCTGGACT
ATACATACTACGTCAACTTCCAGCAGCCAGCAGATGCTGAACGTACCCTGGATACCATGAACTTTGAGGTAATTAAAGGC
AAAACCATTCATATCATGTGGTCTCAGTGGGATCCCTCATTGAGGAAATCAGGAGTTGGGAATGTTTTCATTAAAAACCT
GGATAAATCCATAGACAACAAAGGCACTTTATGACATCTTTTCAGCATCTGGAAACATCTTGTCCTGCAAGGTGGTGTGT
GATGAGAATGGTTCTAAAGACTACGCATTTGTGTACTTTGAGACCCAGGATGCTACCCATAGGGCCTTAGAGAAGATACA
TGGCATGCTTCTCGACCAAAAAGTGTTTGTTGGTAGATTCAAGTCAAGGAAAGAACAGGAAGCAGAACTGGGTGCCAAAG
CTAAGGAATTCAACATTTATATCAAAAACTTTGGAGATGACATGGATGATGAAAGATTGAAGGAAATTTTCAGCAAATAC
GGTAAAACTCTGAGTGTAAAAGTGATGACTGACTCTAGTGGAAAATCCAAAGGTTTTGGTTTTGTGAGTTTTGAGAAACA
TGAGGATGCCAATGAGGCAGTTGAAGAAATGAATGGAAAAGACATCATTGGGAAAATGGTATTTGTAGGCTGAGCACAGA
AGAAAGTTGAACTCTAGGATGAATTAAAATGGAAATTTGAACAGCTGAAACAGGACAGAATTAGCTGCTACCAGGGGGTG
AATCTCTACATTAAGAACCTGGATGAAACCATTTGTGATTAAATATTAAGGAAGTAATTTTCTCCTTTTGGATCAGTTAC
CAGTGCCAAGGTGATACTTGAGGATGGGTAAAGTAAAAGGTTTGGCTTTGTCTGCTCTTCGCCTGATGAGGCTACCAAAG
CAGTGACAGAAATGAATGGGCACATTGTGGGCTCCAAGCCTTTGTACATTGCACTCACACAAAGGAAAGAAGAGAGAAAA
ACCCACCTCACCAATCAGTATATGCAGTGTATTGCAGGAATGAGA

Alignment

ORF - retro_meug_1229 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.82 %
• Parental protein coverage: 64.04 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNASGPGYPMASLYVGDLHPDVTEAMLYEKFSAAGPIMSIRVCRDVSTRRSLGYAY-INFQQPADAERAL
          .N.....YP.ASLYV.DLH.D..EA.LYEKFS.A.......VCRD..TR.SL.Y.Y..NFQQPADAER.L
Retrocopy LNTGATSYPVASLYVVDLHSDIPEATLYEKFSLARLMLFVQVCRDMITRLSLDYTYYVNFQQPADAERTL

Parental  DTMNFEVIKGRPIRIMWSQRDPGLRKSGIGNIFIKNLDDSIDNK-ALYDTFSTFGNILSCKVAYDENGSR
          DTMNFEVIKG..I.IMWSQ.DP.LRKSG.GN.FIKNLD.SIDNK.ALYD.FS..GNILSCKV..DENGS.
Retrocopy DTMNFEVIKGKTIHIMWSQWDPSLRKSGVGNVFIKNLDKSIDNK>ALYDIFSASGNILSCKVVCDENGSK

Parental  GFGFVHFETEDAANQAISTMNGMLLNDRKVFVGHFKSRQEREAELGARVLEFTNIYVKNFKENVDDRCLQ
          ...FV.FET.DA...A.....GMLL.D.KVFVG.FKSR.E.EAELGA...EF.NIY.KNF....DD..L.
Retrocopy DYAFVYFETQDATHRALEKIHGMLL-DQKVFVGRFKSRKEQEAELGAKAKEF-NIYIKNFGDDMDDERLK

Parental  EIFSQFGKTLSVKVMVDENGHSRGFGFVNFEKHEEAQKAVSSMNGKEFGGRVLYVGRAQKKTERQSELKR
          EIFS..GKTLSVKVM.D..G.S.GFGFV.FEKHE.A..AV..MNGK...G....VG.AQKK.E...ELK.
Retrocopy EIFSKYGKTLSVKVMTDSSGKSKGFGFVSFEKHEDANEAVEEMNGKDIIGKMVFVG*AQKKVEL*DELKW

Parental  RFEQMKQERVNRCQGVNLYVKNLDDIIDDEKLRKEFSPYGVITSAKVMTEGGHSKGFGFVCFSSPEEATK
          .FEQ.KQ.R....QGVNLY.KNLD..I.D..LRK.FSP.G..TSAKV..E.G.SK.FGFVC.SSP.EATK
Retrocopy KFEQLKQDRISCYQGVNLYIKNLDETICD*ILRK*FSPFGSVTSAKVILEDG*SKRFGFVC-SSPDEATK

Parental  AVTEMNGRIVCTKPLYVALAQRKEERKAILTNQYMQRISVLR
          AVTEMNG.IV..KPLY.AL.QRKEERK..LTNQYMQ.I...R
Retrocopy AVTEMNGHIVGSKPLYIALTQRKEERKTHLTNQYMQCIAGMR

Legend:

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

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_1229 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1229 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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 4 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000007145	1 retrocopy	retro_meug_426,
Macropus eugenii	ENSMEUG00000007905	6 retrocopies	retro_meug_1165, retro_meug_1229 , retro_meug_1274, retro_meug_1343, retro_meug_419, retro_meug_987,
Microcebus murinus	ENSMICG00000000974	1 retrocopy	retro_mmur_42,
Myotis lucifugus	ENSMLUG00000006324	1 retrocopy	retro_mluc_509,