RetrogeneDB ID: retro_amel_1742

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194156.1:321380..322283(+)
• 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_1742
TTCAGCCTGAAGAGGTATGTGGAAATCGTTAAGGAAGTCAGCACCTCCATTTAAAAAAGTTGGCTCCCACCCCGACACAG
TAGCATCCCTGCCAATTAATGGTTGGAAGGGTGACAACGTGCTGGAGCCAAGTGCTAATATGCCTTGGTTCGAGGGGTGG
AAAGTCACCCATAAAATGACAACGCCAGTGGAACCATGCTACGTGAAAATCTTCATGGCATCTGCCACAACTCATCCAGC
TGGCAAGCCACTTCATCCACCCCTCCAGGACATCCACTAAATTAGAGGTATTGGTACTGTCCCTGTGGACCCAGTGGAGT
CTGATGTTCTCAGACCTGGCATGGTGGTCACCTTGGCTCCAGTCAATATTACAACTGAAGTCAAGTGTGTTGAAATGCAC
CACAACGCTTTGAGAGAAATGCTAGCTCTTCCTCGGGACCACATGGGCTTCAATGCCAAGAACGCATCTGTCAGAAATGT
TCATCGTGGCAACCTGTCTGGTGAGAACAAAAATGACCCACCAATGTACGCAGCTGGTTGTGTGGCTTGGGTGATTATCC
TGAACCATCCAGGCCAGAGCAGTGCTGGCTAGGTACCTATGTCAGATGGTTACATAGCTCATACTGCTTGCAAGTGTGCT
GGGCTAAAGGAGATCGACTGCTGCTCAGGGAAAAAGCAGGAAGATGGCCCCACGTTCTTGAAATCTGTGATGCAGCTGTT
GTTGGTATGGTTGCTGACAAGCCTACCTGTGTTGAGTGCTTCTCTGACTACCCTCCTCTGCGTTATTTTGCTGTTCCTGA
CATGAGACAGACAGTTGCTGTGGGTGTCATCAAAGCAGTGGCCAAGAAGGCTACAGGAACTGGTAAGGTCACCAAGTCTG
CCCAGAACACTCAGAAGGCTAAA

Alignment

ORF - retro_amel_1742 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.16 %
• Parental protein coverage: 64.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  YSQKRYEEIVKEVSTYI-KKIGYNPDTVAFVPISGWNGDNMLEPSANMPWFKGWKVTRK-DGNASGTTLL
          .S.KRY.EIVKEVST.I.KK.G..PDTVA..PI.GW.GDN.LEPSANMPWF.GWKVT.K...NASGT.L.
Retrocopy FSLKRYVEIVKEVSTSI>KKVGSHPDTVASLPINGWKGDNVLEPSANMPWFEGWKVTHK<NDNASGTMLR

Parental  EALDCI-LPP-TRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPVNVTTEVKSVEMHHE
          E.L..I.LP..T.P..KPL..PLQD...I.GIGTVPV..VE..VL.PGMVVT.APVN.TTEVK.VEMHH.
Retrocopy ENLHGI<LPQ<THPAGKPLHPPLQDIH*IRGIGTVPVDPVESDVLRPGMVVTLAPVNITTEVKCVEMHHN

Parental  ALSE--ALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHT
          AL.E..ALP.D..GFN.KN.SV..V.RGN..G..KNDPPM.AAG..A.VIILNHPGQ.SAG..P..D...
Retrocopy ALREMLALPRDHMGFNAKNASVRNVHRGNLSGENKNDPPMYAAGCVAWVIILNHPGQSSAG*VPMSDGYI

Parental  AHIACKFAELKEKIDRRSGKKLEDGPKFLKS-GDAAIVDMVPGKPMCVESFSDYPPLGRFAVRDMRQTVA
          AH.ACK.A.LKE.ID..SGKK.EDGP.FLKS..DAA.V.MV..KP.CVE.FSDYPPL..FAV.DMRQTVA
Retrocopy AHTACKCAGLKE-IDCCSGKKQEDGPTFLKS<CDAAVVGMVADKPTCVECFSDYPPLRYFAVPDMRQTVA

Parental  VGVIKAVDKKAAGAGKVTKSAQKAQKAK
          VGVIKAV.KKA.G.GKVTKSAQ..QKAK
Retrocopy VGVIKAVAKKATGTGKVTKSAQNTQKAK

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_1742 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1742 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 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,