RetrogeneDB ID: retro_amel_1203

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193036.1:39939..41208(+)
• 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_1203
AAACCACCACTCAACCTAAACCAAAATGGGAAAAGGCAAGACTCACATCGATGTCGTCATTGGACACGCAAGTTCTGTCA
GGTCAACCGCTACTGGTCATCTGATCTACAGATGTGGTGGGATCGATACAAGAACTACTGAAAAAATTGAGAAGGAGGCT
CCTGAGATGGGAAAAGGCTCCTTCAGGTACGCCTGGGTCTTGGATCAACTGAAAGCTGAACATGGACGTGGTATCACTAT
TGATACCTCCCTGTGGAAACTGGAGACCAGCAAATATTATGTGACCATCATTGATGCCCCATGACACAGAGACTTAATCA
AAAAGATGATTGAGGCACATCTCAGGCTGACTGTGCTGTCCTGATTGTTGCTGCTGTGTTGGTGAATTTGAAACAGGTAT
CTCCAAGAATGGGGAGAATCGTGAGCATGCCCTTCTGGTTTACACACTGGGTATAAAACAACTAATCGTTGGTGTTAACA
AGATGGATTCCACTAAGCCTCCCTACAGCCAGAAGAGATACGAGGAAATCGTTAAGGAAGTCAGCACCTACATTAAGAAA
ATTGGCTACTGCCCAACACAGTAGCATTTGTGCCAATTTCTGGTTGGGATGGTGACAACGTGCTGGAGCCAAGCGCTAAC
ATGCCTCAGTTCAGGGATGGAAAGTCACCCGTAAAGATGGGAATGCCAGGGGAACCACACTGCTCGAAGCTCTGGATTGC
ATTCTGCCACCAACTCATCCAACTGACAAGCCCTTGCGTCTGCCTCTCCAGGACATCTACAAGATTGGTGGTATTGGTGC
TGTCCCTGTGAGCCAAGTGGAGACTGGTGTCCTTAAACCTGCCATGATGGTCACCTTTGCTCTAGTCAATGCTACAGCTG
AAGTAAAGTCTGCTGAAATGCACCATGAAGCTTTGAACGAGGTTCTTCCCAGGGACAATGTGGGCTTCAATGTCAGAAAC
ATATCTGTCAAAAACATTCGTCGTGGCAATGTAGCTGGTGACAGCAAAAATGACCCACCCATGGAAGCAGCTGGCTTCAC
GGCTCAGGTGATTATCCTGAACCACCCAGGCCAGATCAGTGCTGGGTATGCACCTGTGCTGGATCGTCACACAGCTCACG
TGGCTTGCAAGATTGCTGAGCTGAAGGGGAAGATTGGTCGTCGTTCTGGAAAAAGGCTGGAAAATGGTCCCAAGTTCTTA
AAATCTGGTGATGCTGCCGTCGTTGATACGGTTCCTGGCAAGCCTGTGTGTGTTGAGAGCCTCTCTGAC

Alignment

ORF - retro_amel_1203 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.22 %
• Parental protein coverage: 90.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KPPLNLNQNGKGKDSHI-VVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDK
          KPPLNLNQNGK..DSH..VVIGH..S..ST.TGHLIY.CGGID.RT.EK.EKEA.EMGKGSF.YAWVLD.
Retrocopy KPPLNLNQNGKRQDSHR>VVIGHASSVRSTATGHLIYRCGGIDTRTTEKIEKEAPEMGKGSFRYAWVLDQ

Parental  LKAERERGITIDISLWKFETSKYYVTIIDAPGHRDFIKNMIT-GTSQADCAVLIVAAG-VGEFEAGISKN
          LKAE..RGITID.SLWK.ETSKYYVTIIDAP.HRD.IK.MI..GTSQADCAVLIVAA..VGEFE.GISKN
Retrocopy LKAEHGRGITIDTSLWKLETSKYYVTIIDAP*HRDLIKKMIE<GTSQADCAVLIVAAV<VGEFETGISKN

Parental  GQTREYALLAYTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNP-DTVAFVPISGWNGD
          G..RE.ALL.YTLG.KQLIVGVNKMDST.PPYSQKRYEEIVKEVSTYIKKIGY.P..TVAFVPISGW.GD
Retrocopy GENREHALLVYTLGIKQLIVGVNKMDSTKPPYSQKRYEEIVKEVSTYIKKIGYCP<NTVAFVPISGWDGD

Parental  NMLEPSANMPWFK-GWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVE
          N.LEPSANMP.F..GWKVTRKDGNA.GTTLLEALDCILPPT.PTDKPLRLPLQD.YKIGGIG.VPV..VE
Retrocopy NVLEPSANMPQFR<GWKVTRKDGNARGTTLLEALDCILPPTHPTDKPLRLPLQDIYKIGGIGAVPVSQVE

Parental  TGVLKPGMVVTFAPVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAA
          TGVLKP.M.VTFA.VN.T.EVKS.EMHHEAL.E.LP.DNVGFNV.N.SVK..RRGNVAGDSKNDPPMEAA
Retrocopy TGVLKPAMMVTFALVNATAEVKSAEMHHEALNEVLPRDNVGFNVRNISVKNIRRGNVAGDSKNDPPMEAA

Parental  GFTAQVIILNHPGQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGK
          GFTAQVIILNHPGQISAGYAPVLD.HTAH.ACK.AELK.KI.RRSGK.LE.GPKFLKSGDAA.VD.VPGK
Retrocopy GFTAQVIILNHPGQISAGYAPVLDRHTAHVACKIAELKGKIGRRSGKRLENGPKFLKSGDAAVVDTVPGK

Parental  PMCVESFSD
          P.CVES.SD
Retrocopy PVCVESLSD

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_1203 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1203 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,