RetrogeneDB ID: retro_amel_1855

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194880.1:6015..7372(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000007786
• Aliases: None
• Description: Elongation factor 1-alpha [Source:UniProtKB/TrEMBL;Acc:G1LMH6]

Sequence

>retro_amel_1855
AACATTGTCATCATTGGACACATAGTTTTGAGCAAGTCAATCACTACTGGTCATGTGATCTACAAATATGGTAGGATTGA
CAAAAGGACTATTGTAAAATTTGAGAAGGAGGCTGCTAAGATGGGAAAGGGCTGCTTCAAGTATGCCTGGGTCTTGAATA
AACTGGAAGTTGAATGTTAACATGGTATCACCACTGATACCTCCCCGTGGAAATTTGAAAACAGCAAGTATTATATGACC
ATCATTGATGCCTCAGGACACAGAGACCTTATCAAAAACATGATTACAGGCACATCTCAGGCTGACTGTGATGTCTTATT
GTTGCTGCTGGTATTGTGAATTTGAAGCAGGTATCTCAAAGAATGGGAAGACCCATGAACATGCCCTTTTCACTTACTCC
CTGGGTGTGAAACAATTAATTATTGGTGTTAACAGAATGGATTCCGCTGAGCCACCCTACAACTAGAAGAGATATAAGGA
AATTGTTAAGGAGGTCAGCACCTACATTAAGAAAATTGGCTACAACCCTGACACAGTAGCATCTGTGCCAATTTCTGGTT
GTAATGGTGACAACATGATAGACACAAATATTAACATGCTTTTTGTTTGAGGGATGGAAATTCACCCATAAAGATGGCAA
TGCCTGTGGAACCATGCTGCTTGAAGCCCTGAATTGCATTCTTCCATCAACTCATCCAACTGACAAGCCCTTGTGTCTCC
CCCTCCAGGACATCTACAAAATTGGTGGTATTGGTATTGTCCCTGTGGGTTGAGTGGAGACTCTTGTTCTTAAACCCAGC
ATGGTGGTCACCTTTGCTCCAGTCAATGTTACAACTGAACTCAAGTGTGTCGAAATGCACCAGGAAGCTTGAATAAGACT
ATTCCTGGGGACAATGTGTGCTTCAACGTCAAGAACCTATCTGTCAAAGATGTTCATCATGGTAATGTGGCTGGTGACAG
CAAAAATAACCCACCAATGGAAGCATCTGGCTTCACAGCTTAGGTGATTATCCTGAACCATCCAGACCAAATCAGTGCTG
GATATGTACCTGTGCTGGATTGTCACACAGTTCAAGTTGCTTGCAAGTTTGCAGAGATGAAGGAGAAGATTGATCATCAT
TCTGGAAAAAAGCTGGAAGATGGCCCCATGTTCTTGAAATCTGGTAATGCTGCCATCATTGATATGGTTCCTGGCAAGTC
TATGTGTGTTGAGAGTTTCTCTGACTATTCTCCTCTGGGCCATTTTGCTGCTTGTGATATGAGACAGATGGTTGTTGTGG
GTGTTAAAGCAGTGGACAAGAAGGCAGCTGGAACTGGCAAGGTCACCAAGCCTGCCCAGAAAGCTCAGAAGGCTAAA

Alignment

ORF - retro_amel_1855 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.51 %
• Parental protein coverage: 96.8 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  HIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERGITIDISLW
          .IV.IGH....KS.TTGH.IYK.G.IDKRTI.KFEKEAA.MGKG.FKYAWVL.KL..E...GIT.D.S.W
Retrocopy NIVIIGHIVLSKSITTGHVIYKYGRIDKRTIVKFEKEAAKMGKGCFKYAWVLNKLEVEC*HGITTDTSPW

Parental  KFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVL-IVAAGVG-EFEAGISKNGQTREYALLAYTLGVK
          KFE.SKYY.TIIDA.GHRD.IKNMITGTSQADC.VL.IVAAG...EFEAGISKNG.T.E.AL..Y.LGVK
Retrocopy KFENSKYYMTIIDASGHRDLIKNMITGTSQADCDVL<IVAAGIV<EFEAGISKNGKTHEHALFTYSLGVK

Parental  QLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEPSANMPW-FKGWK
          QLI.GVN.MDS.EPPY..KRY.EIVKEVSTYIKKIGYNPDTVA.VPISG.NGDNM.....NM...F.GWK
Retrocopy QLIIGVNRMDSAEPPYN*KRYKEIVKEVSTYIKKIGYNPDTVASVPISGCNGDNMIDTNINMLF>FEGWK

Parental  VTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPVNV
          .T.KDGNA.GT.LLEAL.CILP.T.PTDKPL.LPLQD.YKIGGIG.VPVG.VET.VLKP.MVVTFAPVNV
Retrocopy FTHKDGNACGTMLLEALNCILPSTHPTDKPLCLPLQDIYKIGGIGIVPVG*VETLVLKPSMVVTFAPVNV

Parental  TTEVKSVEMHHEA-LSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHPGQIS
          TTE.K.VEMH.EA.L....PGDNV.FNVKN.SVKDV..GNVAGDSKN.PPMEA.GFTA.VIILNHP.QIS
Retrocopy TTELKCVEMHQEA<LNKTIPGDNVCFNVKNLSVKDVHHGNVAGDSKNNPPMEASGFTA*VIILNHPDQIS

Parental  AGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVESFSDYPPLGRF
          AGY.PVLDCHT...ACKFAE.KEKID..SGKKLEDGP.FLKSG.AAI.DMVPGK.MCVESFSDY.PLG.F
Retrocopy AGYVPVLDCHTVQVACKFAEMKEKIDHHSGKKLEDGPMFLKSGNAAIIDMVPGKSMCVESFSDYSPLGHF

Parental  AVRDMRQTVAVGVIKAVDKKAAGAGKVTKSAQKAQKAK
          A..DMRQ.V.VGV.KAVDKKAAG.GKVTK.AQKAQKAK
Retrocopy AACDMRQMVVVGV-KAVDKKAAGTGKVTKPAQKAQKAK

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_1855 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1855 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 10 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007786	14 retrocopies	retro_amel_1064, retro_amel_1072, retro_amel_1079, retro_amel_1140, retro_amel_1167, retro_amel_1203, retro_amel_1227, retro_amel_1283, retro_amel_1371, retro_amel_160, retro_amel_1742, retro_amel_1797, retro_amel_1855 , retro_amel_200,
Canis familiaris	ENSCAFG00000013249	1 retrocopy	retro_cfam_1007,
Dipodomys ordii	ENSDORG00000009629	1 retrocopy	retro_dord_509,
Equus caballus	ENSECAG00000022260	1 retrocopy	retro_ecab_802,
Erinaceus europaeus	ENSEEUG00000000342	3 retrocopies	retro_eeur_407, retro_eeur_492, retro_eeur_625,
Loxodonta africana	ENSLAFG00000028081	1 retrocopy	retro_lafr_651,
Monodelphis domestica	ENSMODG00000018533	4 retrocopies	retro_mdom_1053, retro_mdom_1146, retro_mdom_311, retro_mdom_792,
Mus musculus	ENSMUSG00000037742	15 retrocopies	retro_mmus_1349, retro_mmus_1518, retro_mmus_1667, retro_mmus_1783, retro_mmus_1816, retro_mmus_1849, retro_mmus_1850, retro_mmus_1864, retro_mmus_1909, retro_mmus_2363, retro_mmus_2583, retro_mmus_2902, retro_mmus_3249, retro_mmus_480, retro_mmus_483,
Ictidomys tridecemlineatus	ENSSTOG00000007687	4 retrocopies	retro_itri_1509, retro_itri_1740, retro_itri_1816, retro_itri_195,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,