RetrogeneDB ID: retro_amel_651

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192546.1:1679833..1680722(-)
• Located in intron of: ENSAMEG00000012559

Retrocopy information

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

Parental gene information

• Parental gene symbol: ELL2
• Ensembl ID: ENSAMEG00000010607
• Aliases: None
• Description: elongation factor, RNA polymerase II, 2 [Source:HGNC Symbol;Acc:17064]

Sequence

>retro_amel_651
GAGAACTCCCTGGGAGCAATTCTGCAACAGATAGCCAATCTGAATCCTAAAAACCTGTCATACACCTTAAAGGATTATGT
TTTTAAAGTGCTTCGAAAAGACTGGCCCAGATGCAGTGAAATAGAAATAGAACGTCGTTAGGCAGTGCTCTCGAGCGCAC
TAAATCTATCTCAGAATGCTGCCAGCACCAGCCATTCAGGATCTCTTGCATGTTCTAAAGGAGACGCTGCCTCTTCTCCT
CAGAATCGGCTTTGAGATTCAGATTTCATTGATCTTTAATGACTAAAAAAACCTTGAATATCTTACTTGACAGGTCGAGT
GCTTCCAACATTAAATGATCACTTGAATCCCTCCAGTGAAAAATCTGTTCCAGACGTCCTGTCTCCTGCAGCCGCTGCCG
TCCCTGCCCCTCTACCGCTGCTTTCAACCCACCTGCCCGGCTCCAATCCTCCTCTGATTCTAAATTCTAACTCCAGTTCC
CCTAGCACTCCAGCAGGCCAGGGGACCCAAGACCTACCTGTTGACAGTTTTAATCAAAACACCAGTATCTATCAGGACCA
ACAAGATAAATATACCTCTAGGCCTTCTCTGGAAACCCTAACCCTGGTTCAGTTCTACTGAAGTGTCCAAAGCCTGTGGA
AGAAAACCATTCATTGTCTCACAAAAAGTCCAAAGAAGTCTAAAAACCGAAGGAAAAGGCCAAATTGAAATGCACGACAT
TGAGACAACTGAAGAAAAGGAAGAGGGCCTTAAAAGAGATGAGAAAATTGCCAAGCTGAATAACTCCAGTCCTGATTCCA
TTGAAGGAGTTAAAGAGGGTTGTACTGCCTCCACCAGGCCTTTTTCAACAACTGAACTCCCAGATTATTTGACAAAATAA
ATTGCTATT

Alignment

ORF - retro_amel_651 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.09 %
• Parental protein coverage: 50.59 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KNSLGAILQQVANLNPKDLSYTLKDYVFKELQRDWPGYSEIDRRSLESVLSRKLNPSQNAASTSRSESPV
          .NSLGAILQQ.ANLNPK.LSYTLKDYVFK.L..DWP..SEI.......VLS..LN.SQNAASTS.S.S..
Retrocopy ENSLGAILQQIANLNPKNLSYTLKDYVFKVLRKDWPRCSEIEIERR*AVLSSALNLSQNAASTSHSGSLA

Parental  CSNRDAASSPQKRLLDSDFIDPLMNKKARISHLTNRVPPTLNGHLNPTSEKSAAGHLPPPAAAAIPTPPP
          CS..DAASSPQ.RL.DSDFID....KK..IS.LT.RV.PTLN.HLNP.SEKS....L..PAAAA.P.P.P
Retrocopy CSKGDAASSPQNRL*DSDFIDL**LKKP*ISYLTGRVLPTLNDHLNPSSEKSVPDVL-SPAAAAVPAPLP

Parental  LPPTHLPVSNPPQTVNSNSNSPSTPEGRGTQDLPVDSFSQNSSIYEDQQDKYTSRTSLETLP-PGSVLLK
          L..THLP.SNPP...NSNS.SPSTP.G.GTQDLPVDSF.QN.SIY.DQQDKYTSR.SLETL..PGSVLLK
Retrocopy LLSTHLPGSNPPLILNSNSSSPSTPAGQGTQDLPVDSFNQNTSIYQDQQDKYTSRPSLETLT<PGSVLLK

Parental  CPKPMEENHSMSHKKSKKKSKKHKE-KDQIKKHDIEMTEEKEEDLKREEEIAKLNNSSPDSNEGILEGCT
          CPKP.EENHS.SHKKSK...K..KE.K.QI..HDIE.TEEKEE.LKR.E.IAKLNNSSPDS.EG..EGCT
Retrocopy CPKPVEENHSLSHKKSKEV*KP-KE<KGQIEMHDIETTEEKEEGLKRDEKIAKLNNSSPDSIEGVKEGCT

Parental  ASTEPSSTIELPDYLIKYIAI
          AST.P.ST.ELPDYL.K.IAI
Retrocopy ASTRPFSTTELPDYLTK*IAI

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_651 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_651 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.

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010607	1 retrocopy	retro_amel_651 ,
Dasypus novemcinctus	ENSDNOG00000005103	1 retrocopy	retro_dnov_1413,
Equus caballus	ENSECAG00000022933	1 retrocopy	retro_ecab_1092,
Homo sapiens	ENSG00000118985	1 retrocopy	retro_hsap_459,
Nomascus leucogenys	ENSNLEG00000014192	1 retrocopy	retro_nleu_881,
Pongo abelii	ENSPPYG00000015647	1 retrocopy	retro_pabe_1757,
Pan troglodytes	ENSPTRG00000017090	1 retrocopy	retro_ptro_346,